I should start by saying I am not meaning this to be just another monk fix. It is more meant to feel like a Final Fantasy Monk than just fix a broken class. For that, there are a lot of Monk fixes out there, several from the playground, and if you really wanted to use an official 'fix' there's always unarmed swordsage.
Class Goals:
This is meant to emulate the Monk or Black Belt classes from Final Fantasy, namely FF1-5. This entails having very high HP and damage despite not getting the perks of weaponry or armor. There are other minor abilities these classes typically get, like a Counter ability or Kick attack that hits everything, but as those are incorporated in various feats, those will be optional additions rather than granted abilities. Most Monks typically don't have any magical abilities (in FF1 and FF4, it's actually the only class with 0 spellcasting ability), meaning no Dimension Door shenanigans. Minor ki powers will show up for the sake of coolness if it very directly enables the class's combat ability, but nothing nearly as flashy as Dimension Door or Etherealness.

The Crystal Monk

"Weapons are weak. Armor is fragile. I forge my body and mind in unbreakable crystal." - Yang Fang Leiden, Crystal Monk of the Kingdom of Fabul

Crystal Monks strive for enlightenment through balance. Their deep meditation grants them prowess beyond that of normal combatants. The zen they achieve fuels their entire being. True greatness can be found only in soundness of body and mind. A Crystal Monk relies only on themselves, not on superfluous pieces of equipment or enhancements.
Adventures: Crystal Monks typically adventure as a way to explore themselves more fully and to test the extent of their abilities. Others strive to show others the truth of their ways by venturing out and taking on students. Many will also take on instructions by their masters that include crossing the country side for some monumental task.
Characteristics: Crystal Monks tend to be somewhat reserved. They normally think first and act second, rarely acting rashly or spontaneously. They believe heavily in teamwork but moreso in everyone pulling their own weight; if someone takes more than they give in a group, they disrupt the balance which is best.
Alignment: With the endless emphasis on balance, Crystal Monks always find some level of neutrality to be best. Many naturally lean to lawfulness due to their strict codes of discipline, but that is not to say that many to not find pure chaos and flux to have its own natural balance. Good and evil Crystal Monks are less common than lawful or chaotic, but a follower of both holiness and balance is not shunned or outcast.
Religion: Crystal Monks tend not to devote too much time or energy to worship deities. Gods of balance and wisdom are most likely to have Crystal Monk followers. Those who embody pure ideals of a certain alignment, such as St. Cuthbert focusing on law and nothing else, or Pelor only caring of good rather than law or chaos, also appeal to Crystal Monks who share these alignments.
Background: Crystal Monks often start their path of balance due to some tragic event in their lives. A lone survivor of a town destroyed by forces of evil might become a neutral good Crystal Monk, or a warrior outcast by society due to radical ideals might become a chaotic neutral Crystal Monk. The majority of aspirants find some mentor who has already attained a level of balance in their lives to teach them, either in monasteries or small groups of nomads. Many Crystal Monks eventually take on students of their own.
Races: Races which value both mental advancement and physical excellence often produce large quantities of Crystal Monks. Those that naturally form communities might found a monastary, while nomadic races form small tribes of ascetics. Any race, savage or refined, has the potential of Crystal Monks in their numbers.
Other Classes: Crystal Monks value the company of anyone who does not offend their sense of balance. Mages that seek knowledge, priests of neutral deities, those who strive to preserve the balance of nature all make good companions for Crystal Monks. Zealots who believe in narrowly defined doctrines, scoundrels who rely on trickery, warriors that depend on excessive equipment, or spellcasters who neglect anything but powers of arcane or divine source focus their energies too much to get along with Crystal Monks easily unless they are very open minded.
Role: Crystal Monks are most commonly front-line combatants. Above all else, their honed bodies and minds excel at being martial artists. Still, some find non-combat roles to fill, such as being a group's scout or face, and many try to teach their ways to others. These roles are seen much less frequently, even then usually coupled with a focus on fighting.

{table=head]Level|BAB|Fort|Ref|Will|Special|Flurry of Blows|Unarmed Damage|AC Bonus|Crystal Step
1st|+0|+2|+2|+2|Crystal combatant, flurry of blows, stunning fist|-1/-1|1d6|+0|+0 ft.
2nd|+1|+3|+3|+3|Bonus feat, evasion|+0/+0|1d6|+0|+0 ft.
3rd|+2|+3|+3|+3|Crystal step|+1/+1|1d6|+0|+10 ft.
4th|+3|+4|+4|+4|Ki pool (magic)|+2/+2|1d8|+1|+10 ft.
5th|+3|+5|+5|+4|Crystal descent, unarmed augmentation|+3/+3|1d8|+1|+10 ft.
6th|+4|+5|+5|+5|Bonus feat|+4/+4/-1|1d8|+1|+20 ft.
7th|+5|+5|+5|+5|Crystal health|+5/+5/+0|1d8|+2|+20 ft.
8th|+6/+1|+6|+6|+6|Ki pool (adamantine)|+6/+6/+1/+1|1d10|+2|+20 ft.
9th|+6/+1|+6|+6|+6|Crystal defense, improved evasion|+7/+7/+2/+2|1d10|+2|+30 ft.
10th|+7/+2|+7|+7|+7|Bonus feat, improved unarmed augmentation|+8/+8/+3/+3|1d10|+2|+30 ft.
11th|+8/+3|+7|+7|+7|Crystal body|+9/+9/+4/+4/-1|1d10|+2|+30 ft.
12th|+9/+4|+8|+8|+8|Ki pool (aligned)|+10/+10/+5/+5/+0|2d6|+3|+40 ft.
13th|+9/+4|+8|+8|+8|Crystal soul|+11/+11/+6/+6/+1|2d6|+3|+40 ft.
14th|+10/+5|+9|+9|+9|Bonus feat|+12/+12/+7/+7/+2|2d6|+3|40 ft.
15th|+11/+6/+1|+9|+9|+9|Crystal stride, greater unarmed augmentation|+13/+13/+8/+8/+3/+3|2d6|+3|+50 ft.
16th|+12/+7/+2|+10|+10|+10|Ki pool (metalline)|+14/+14/+9/+9/+4/+4|2d8|+4|+50 ft.
17th|+12/+7/+2|+10|+10|+10|Crystal mind|+15/+15/+10/+10/+5/+5|2d8|+4|+50 ft.
18th|+13/+8/+3|+11|+11|+11|Bonus feat|+16/+16/+11/+11/+6/+6/+1|2d8|+4|+60 ft.
19th|+14/9/+4|+11|+11|+11|Crystal sense|+17/+17/+12/+12/+7/+7/+2|2d8|+4|+60 ft.
20th|+15/+10/+5|+12|+12|+12|Crystal enlightenment, ki pool (force)|+18/+18/+13/+13/+8/+8/+3|2d10|+5|+60 ft.
Abilities: Wisdom is the most important ability for you, fueling nearly all your abilities. Dexterity and Constitution help with combat, while Intelligence helps with your large skill list.
Alignment: Any neutral.
Hit Die: d8.
Class Skills: Balance, Climb, Craft, Escape Artist, Jump, Hide, Intimidate, Knowledge (History), Knowledge (Nobility and Royalty), Knowledge (Religion), Listen, Move Silently, Perform, Profession, Ride, Search, Sense Motive, Spot, and Swim.
Skill Points at 1st level: (6 + Int modifier) x 4.
Skill Points at each additional level: 6 + Int modifier.

Crystal Monk Features:
Weapon and Armor Proficiency: As Monk.

Ex-Monks: A Monk who strays from the path of their meditation loses all class features except for weapon proficiencies. This occurs if you take a non-neutral alignment or act in a way that gravely contradicts your alignment, and you cannot take additional levels until you Atone. Similarly, if you wear armor or wield a shield, you lose all class features until you remove the offending item.

Flurry of Blows (Ex): As Pathfinder Monk.

Stunning Fist: At 1st level, you gain Stunning Fist as a bonus feat.

Crystal Combatant (Ex): A Monk draws strength from arduous meditation and training. At 1st level, you gain Improved Unarmed Strike as a bonus feat. Your attacks made with Unarmed Strikes may be with either fist interchangeably or even from elbows, knees, and feet. Neither hand is considered off-hand for attack or damage rolls. Your unarmed strikes deal lethal damage, though you can choose to deal nonlethal damage instead with no penalty on your attack roll. Your unarmed strike is treated as both a manufactured weapon and a natural weapon for the purpose of spells and effects that enhance or improve either manufactured weapons or natural weapons. Your unarmed strikes can deal bludgeoning, slashing, or piercing damage as you choose.
You deal more damage with your unarmed strikes than normal member of your race and size category (see below). If you have a natural attack, you treat your Unarmed Strike as if your size had increased by one category. However, you may not use a natural attack as part of your Flurry of Blows even if it would deal more damage than your (now improved) unarmed strike. Similarly, you may take the Improved Natural Attack feat to increase your unarmed strike damage by one size category. You cannot increase the damage of your unarmed strike by more than one size category in these ways.

Monk Size and Unarmed Damage by Class Level

When unarmored and unencumbered, you add your Wisdom modifier to your AC. In addition, you gain a +1 bonus to AC every four Monk levels. These bonuses to AC apply even against touch attacks or when you are flat-footed, but not when you are immobilized or helpless. Additionally, when making an unarmed strike, you may choose to make the damage bludgeoning, slashing, or piercing. Finally, you gain bonus hit points equal your Wis modifier X your Monk level. As you level, you gain additional bonuses from your dedication to your meditation.
This works as a core Monk's AC Bonus and Unarmed Strike with the following changes:
  • You gain hit points equal to your Wisdom X class level.
  • Unarmed Strikes can deal bludgeoning, slashing, or piercing damage.
  • Natural attacks still can't be used in Flurry of Blows, but they increase the size category of your unarmed strike as if you had taken the Improved Natural Attack feat to do so. Having both a natural attack and the Improved Natural Attack feat only increases the size of your unarmed damage one time.

Bonus Feat: At 2nd level, and every 4 levels thereafter, you may select a bonus feat. These feats must be taken from the following list: Combat Reflexes, Deflect Arrows, Dodge, Improved Grapple, Throw Anything (CWr), Weapon Focus (Unarmed Strike), Yolanda's Sense (RotW), and Zen Archery (CWr). At 6th level, the following feats are added to the list: Expanded Ki Pool (CSc), Extra Stunning (CWr), Improved Bull Rush, Improved Disarm, Improved Feint, Improved Sunder, Improved Trip, Mobility, Power Critical (Unarmed Strike), and Weapon Specialization (Unarmed Strike). At 10th level, the following feats are added to the list: Fiery Fist (PHB2), Fists of Iron (CWr), Improved Critical (Unarmed Strike), Karmic Strike (CWr), Rapid Stunning (CWr), Roundabout Kick (CWr), Snatch Arrows, Spring Attack, and Whirlwind Attack. A monk need not have any of the prerequisites normally required for these feats to select them.

Evasion (Ex): As Monk.

Crystal Step (Ex): Beginning at 3rd level, your gain improved means of movement through your deep meditation. You gain +10 foot bonus to your land speed every 3 levels of Monk (+10 at 3rd, +20 at 6th, etc.) and half of this bonus to any other movement speeds (such as burrow, climb, fly, or swim) you have. This does not grant you any additional movement methods you do not already possess.

Ki Pool (Su): At 4th level, you gain a pool of ki points, supernatural energy you can use to accomplish amazing feats. The number of points in your ki pool is equal to 1/2 your Monk level + you Wisdom modifier. As long as you have at least 1 point in your ki pool, you can make a ki strike. When making a ki strike, you may use your Wisdom modifier in place of your Strength modifier for purposes of attack and damage rolls. At 4th level, ki strike allows your unarmed attacks to be treated as magic weapons for the purpose of overcoming damage reduction.
Ki strike improves with your Monk level. At 8th level, your unarmed attacks are also treated as adamantine weapons for the purpose of overcoming damage reduction and bypassing hardness. At 12th level, your unarmed attacks are treated as aligned weapons for the purpose of overcoming damage reduction. The alignment matches your alignment (chaotic, evil, good, or lawful). If you have none of these alignments, you may choose any one type. At 16th level, your unarmed attacks are treated as cold iron and silver weapons for the purpose of overcoming damage reduction. At 20th level, your unarmed attacks are treated as pure force rather than physical damage, ignoring all damage reduction, miss chances from etherealness and incoproreality, and any other effect that is bypassed by force effects.
By spending 1 point from your ki pool, you can make one additional attack at your highest attack bonus when making a flurry of blows attack. In addition, your can spend 1 point to increase your speed by 20 feet for 1 round. Finally, you can spend 1 point from your ki pool to give yourself a bonus equal to your Wis modifier to any ability score for purposes of ability checks or skill checks for 1 round. Each of these powers is activated as a swift action. You gain additional powers that consume points from your ki pool as you gain levels.
The ki pool is replenished each morning after 8 hours of rest or meditation; these hours do not need to be consecutive.

Crystal Descent (Ex): Beginning at 5th level, treat any fall damage you take as if the fall were 10 feet shorter per two Monk levels.
Additionally, as an immediate action, you may spend 1 ki point to grant yourself feather fall as the spell. This is a supernatural ability that uses your Monk level as your caster level.

Unarmed Augmentation (Su): Beginning at 5th level, a Monk is able to channel their ki to enhance their unarmed strikes. Once per day by meditating for 10 minutes, you can spend 1 ki point to grant your unarmed strikes any special ability whose market price is equivalent to a +1 bonus or up to 2,000 gp, such as flaming or everbright.This enhancement lasts for 24 hours and affects all of your unarmed strikes as if they were the same weapon. You cannot spend more than 1 ki point to grant enhancements to your unarmed strike in a single day.

Crystal Health (Ex): At 7th level, you gain immunity to all diseases.
Additionally, as an standard action, you may spend 2 ki points to heal yourself a number of hit points of damage equal to your Monk level. This is a supernatural ability.

Crystal Defense (Ex): At 9th level, you gain a percent chance to negate precision damage equal to 5 X your Monk level, and you gain DR 5/adamantine and magic.
Additionally, as an immediate action, you may spend 2 ki points to make an attack of opportunity against any creature that made a successful melee attack or melee touch attack against you. This does not grant you additional attacks of opportunity than you normally have. The opponent that hits you must be in your threatened area.

Improved Evasion (Ex): As Monk.

Improved Unarmed Augmentation (Su): Beginning at 10th level, you can use your unarmed augmentation to enhance your unarmed strikes with any special abilities whose combined market price is equivalent to a +3 bonus or up to 18,000 gp, such as speed, by spending 1 ki point for each +1 bonus or each 6,000 gp of the market price. For example, a 10th level Monk can meditate for 10 minutes and spend 3 ki points to grant their unarmed strikes the flaming burst and shadowstrike properties for the day. You cannot spend more than 3 ki points to grant enhancements to your unarmed strike in a single day.

Crystal Body (Ex): At 11th level, you gain immunity to all poisons. You no longer take penalties to ability scores for aging and cannot be magically aged. Any such penalties you have already taken, however, remain in place. Age bonuses still accrue, and you still die of old age.
Additionally, as an immediate action, you may spend 1 ki point to grant yourself a bonus equal to your Wisdom modifier on checks made for combat maneuvers rolls (such as making or resisting a bull rush, disarm, or grapple attempt) for 1 round. This is a supernatural ability.

Crystal Soul (Ex): At 13th level, you gain spell resistance equal to 10 + your Monk level.
Additionally, as an immediate action, you may spend 1 ki point to grant yourself a bonus equal to your Wisdom modifier on saving throws against spells and spell-like effects for 1 round.

Crystal Stride (Ex): Beginning at 15th level, as a move action, you can run up or down a vertical surface a total distance of your move speed without making a climb check. You can only use this ability once per round. If you do not reach the top of the vertical surface or find a suitable hand- or foothold, you must make a Climb check appropriate to the surface. If you succeed on the check, you can use this ability again in the next round. Otherwise you fall or make no progress, as determined by the check result.
Additionally, as a standard action, you may spend 2 ki points to grant yourself air walk, spider climb or water walk as the spells. This is a supernatural ability that uses your Monk level as your caster level.

Greater Unarmed Augmentation (Su): Beginning at 15th level, you can use your unarmed augmentation to enhance your unarmed strikes with any special abilities whose combined market price is equivalent to a +5 bonus or up to 50,000 gp, such as vorpal, by spending 1 ki point for each +1 bonus or each 10,000 gp of the market price. For example, a 15th level Monk can meditate for ten minuets and spend 4 ki points to grant their unarmed strikes the ghost touch, holy, and keen properties for the day. You cannot spend more than 5 ki points to grant enhancements to your unarmed strike in a single day.

Crystal Mind (Ex): At 17th level, you gain immunity to charm, compulsion, and fear effects.
Additionally, as a standard action, you may spend 3 ki points to grant yourself mind blank as the spell. This is a supernatural ability that uses your Monk level as your caster level.

Crystal Sense (Ex): At 19th level, you blindsense to 60 ft.
Additionally, as a swift action, you may spend 1 ki point to mark an opponent hit with your unarmed strike for a number of rounds equal to your Wisdom modifier. While marked, you know exactly where the target is as long as it is on the same plane as you, and you are treated as having blindsight to determine its precise location anywhere within 120 ft.

Crystal Enlightenment: At 20th level, a Monk becomes a magical creature. Your type changes to Outsider (native) rather than as your normal creature type.
Additionally, your damage reduction increases to 10, and the nature of your damage reduction improves to adamantine and the alignment opposite of your aligned ki strike (DR 10/adamantine and chaotic if you have Ki pool (lawful), DR 10/adamantine and good if you have Ki pool (evil), etc.). You also gain immunity to nonlethal damage.
Finally, you can use your unarmed augmentation to enhance your unarmed strikes with any special abilities whose combined market price is equivalent to a +10 bonus or up to 200,000 gp by spending 1 ki point for each +1 bonus or each 20,000 gp of the market price. You cannot spend more than 10 ki points to grant enhancements to your unarmed strike in a single day.

Notes on Class Abilities:
Starting with a Monk as the template of martial artist, there are a few problems the class faces before it would become a viable front-line combatant.
1. MAD
The problem: A Monk needs Strength, Dexterity, Constitution, and Wisdom to function. You could attempt to remove Strength with a few workarounds (Weapon Finesse, Intuitive Strike, being ranged), but that often falls short and requires a lot of extra effort to be on par with another melee class. Without armor, you need Dexterity, but you could try working without it. A d8 on a melee class means Constitution is pretty essential. Wisdom powers... everything flavorful and functional to a monk.

The solution: Make Wisdom the key stat to more than just AC. Core Monks get a handy feature having Wisdom replace its armor, but how about making it replace all of the Monk's neglected areas of combat? Give Wisdom to attack, damage, and hitpoints. Suddenly, a Monk can dump Strength, flavorful since they rely on meditation over brute force. They can make Constitution a mediocre stat, again relying on meditation to help them power through the pain. Beyond that, there is a ki ability that lets you add your Wisdom modifier to ability and skill checks for 1 round, letting you further bypass MAD a few times per day. The class now needs a high Wisdom, a good Dexterity, and a mediocre Constitution score to function.

2. Damage Reduction
The problem: DR quickly cripples a Monk. While their ki strike abilities are meant to help with this, making your fists magic, lawful, and adamantine only helps in a handful of situations. A Zombie, one of the weakest undead monsters out there, stops a Monk with DR/slashing. Any alignment other than chaotic similarly gets in the way. Bypassing DR is important to any Monk who emphasizes attacking multiple times (i.e. all of them).

The solution: Core Monks get a little help bypassing DR with ki abilities. Let's take this ability and run with it. First, make Unarmed Strike deal bludgeoning, slashing, and piercing damage from the start. Keep magic, aligned, and adamantine in there (not in that order, just for preference and flavor), and add cold iron and silver in as well. Make it finish as a force effect, bypassing any and all damage reduction, even DR/-.

3. Weapon Enhancements
The problem: Level 4 core Monks have a possible edge over other melee types by being able to overcome DR/magic when others might still be stuck with masterwork. However, nicer DMs will give out magic weaponry at this point or soon thereafter, and even then the monk still doesn't benefit from masterwork attack bonus. An Amulet of Mighty Fists will help here for a ridiculous amount of gold, and even then you can't get flashy upgrades like Flaming or Keen.

The solution: Ki cures all wounds, doesn't it? The class gets a 1/day, 24 hour duration weapon enhancement for their fists that mimics the Artificer infusion Personal Weapon Augmentation that uses ki according to the strength of the upgrade.

Other tweaks from Monk:
  • Alignment:
    Switching the class alignment restriction from any Lawful to any Neutral was personal choice. I see Monk and think zen, balance, and meditation. If you want to play a Good core Monk, you're stuck with lawful stoopid. It also allows for more versatility with aligned kistrikes.
  • Skills:
    Giving 6+Int skill points is simply to help with the large skill list the class has. I don't see the class needing a decent Int score to be worth while.
  • Flurry of Blows, Stunning Fist, Evasion, and Improved Evasion:
    Standard Monk stuff. No change here.
  • Crystal Combatant:
    This is the standard Monk package with a couple extra benefits.
    I added the function that Unarmed Strike can deal bludgeoning, slashing, or piercing damage to help with DR. I know there's a feat out there for this, but I don't see the point of having to waste a feat for such a bland mechanic. I also added that if you have a natural attack you get bumped up one size category for dealing damage, basically giving them Improved Natural Attack for Unarmed Strike. I hated that creatrues that already had good natural weapons were actually penalized for going Monk; this way, if a werecrocodile were to want to go Monk, they don't lose the benefit of part of their template.
    Now before I get flak for WIS * level -> HP being way too much, I'd like to point out three things: 1. this is meant to be a Final Fantasy Monk, which traditionally has one of the highest hit points in the game, 2. this is still based on core Monk, so way too good only makes it average, and 3. this actually only puts a Monk roughly on par with a Barbarian. Consider a Dwarf focusing on HP that rolls two 18's for stats. As a level 1 Barbarian with 20 Con, he has 17 hit points. As a level 1 Crystal Monk with 20 Con and 18 Wis has 17 hit points, but has lower AC, conditional DR instead of DR/-, and won't hold a candle to the eventual damage a Great Axe + Leap Attack + Shock Trooper Barbarian would have. Yes, 1d8+9 > 1d12 + 5, but you're dedicating two good rolls to HP for a Monk and only one for a Barbarian. This is meant to give the class a chance to not depend on Con; if your approach is to make Con a primary stat anyway and make more MAD, then you can have a huge amount of hit points.
  • Bonus Feats:
    This is heavily borrowed from the pathfinder monk, but I've added in a lot of 3.5 feats that I find helpful for the martial artist build. More than anything this just adds some variability to the class.
  • Crystal abilities:
    These are meant to mimic a lot of class features / ACFs for Monk as well as ki upgrades. Step grants benefits all movement speeds, making it more useful to stranger races than boring old core races. Descent gives slow fall that turns into feather fall with ki. Health, Defense, Body, and Mind give immunities that also function as ki defense upgrades. Sense upgrades to sensing the target's ki for better tactics. Stride upgrades Step to incorporate an ACF from Dungeonscape while giving fun alternatives to prevent terrain from getting in the way of melee combat.
  • Ki Pool:
    The various unarmed bonuses are meant to help the class overcome DR more easily (as described above).
  • Unarmed Augmentation:
    By giving the class weapon enhancements to their fists based on ki expendatures lets the class use their fists without being majorly gimped. No need for fancy weapons that may or may not use Unarmed Strike damage, no need for workarounds that can grant fist enhancements. The ability turns to Personal Weapon Augmentation from Artificer for base mechanics, altered obviously to be 1/day and 24 hours.
  • Crystal Enlightenment:
    The native outsider change keeps with the core Monk, but hopefully this really feels like a capstone. DR 10/adamantine and alignment, heavy fortification, and immunity to nonlethal damage all aids front-line combat. Epic level weapon enhancements (at a steep ki cost) lead for very fun combats, having Keen Holy Flaming Burst Vampiric Bodyfeeder fists/knees/forehead of pure force is... neat.

Hopefully this boils down to a fun melee class that keeps the feel of martial artist badass. Let me know what you think of the class as a whole, individual abilities, and flavor.