Okay, so now that I've gotten a few responses I have a direction in which to explain my thoughts behind this. In no particular order:

The removal of spellcasting from spellcasting monsters wasn't an issue of balance from shapeshifting or summoning/calling. It was actually about complexity needed to run. I find it weird that a dragon (for example) has all these natural attacks and a breath weapon and senses and flight and SLAs, all of which add a bit of complexity, yet it also has all these spells, most of which it's never going to use but still raise its CR for some reason. If I want a NPC to have spellcasting, I want it to be from a spellcasting class rather than a racial feature in addition to a bunch of other things. If it's a NPC appearing in more than just one fight and thus has more than a few rounds to use its abilities, I'd rather it have an ally doing the spellcasting rather doing it itself. This is still a matter of personal preference though.

Long range magical teleportation is accessible via the Travel Domain and either Arcane Disciple or an Adept (the Religious Adept variant from Eberron Campaign Setting where one domain's spells are added to a class list is a built in part of the Adept here, though I didn't list it. Might go back on that though.) Runestaffs or other magic items can also be used for other classes, though it's often easier to hire a specialist if you're not going to be doing it that often. Short range teleportation like Dimension Door is much more common, not only from class spell lists and magic items but also from dragonmarks and other bits and bobs. Psionic teleportation is also fairly easy to access either via Psychic Warrior or the Expanded Knowledge feat.

The thing about magic items being considered different prices when determining availability is taken from weapon and armor templates from DMG2. I wanted a way to simulate a market economy while not upsetting WBL, and I wanted a compromise between "Here's the magic items available, take it or leave it." and "This small shop has every possible item priced below the community size limit." Players can still order custom items, but they shouldn't expect some obscure, custom, or rare item to be available just because they're in a large enough community.

The xp for encounters going up over the course of the day is to solve the 15 minute adventuring day problem. D&D 3.5 often balanced things by giving some build options more powerful abilities in exchange for few daily uses while giving other build options weaker abilities in exchange for being able to do it all day. This system gets ruined when the party can just blow all their daily abilities in the first fight than wait 24 hours to do it again. Putting the burden on adventure designers or DMs to create a reason for the party to not do this is somewhat unfair when this issue should be fixed within the system itself. Now the party has to consider the increasing XP awards with the risk of overextending themselves. The idea of increasingly challenging encounters being worth more than the same encounters in reverse wasn't intentional, but I like it anyway. In the latter case, PCs can use more of their daily abilities in the first fight since they're closer to retreat if necessary, whereas in the former case it's unknown how many of their daily abilities they saved for the tougher fight.

The Hide and Move Silently rules are more to resolve ambiguities in the base rules than to make new ones. Making one of the checks is a move action, but can you make both with the same move action? But it's -20 to make one when you're attacking, running, or charging, so when is those actions are you using your move action? If you move over with a move action and you succeed on your stealth checks, and then you attack, does your previous stealth check retroactively get a -20 penalty? Or does it apply to your next move action? If you don't move stealthily next round, how long does the -20 penalty last? Running and charging are full round action in which you move, so the penalty can apply to that movement? Hide and Move Silently checks are opposed by Spot and Listen checks, but Spot and Listen checks take a move action, so can take up one of the enemy's move actions just by hiding whether they're looking for you or not? All these questions aren't really resolved in the base rules, so I decided to clarify them. The +10 for not moving is because of the penalty for moving too quickly and the +20 bonus for an invisible creature not moving (on top of the +20 for being invisible). I wanted there to be some sort of bonus for using a move action with no movement, especially since it's somewhat difficult to get cover or concealment in the middle of combat. Now a Rogue in melee in an Obscuring Mist can give up iterative attacks in exchange for sneak attack (plus no Dex to AC and the +2 for invisibility), assuming they beat the Spot check. The use of move actions for things other than moving is also a slight buff to standard action based builds (e.g. casters, martial adepts, AoO builds, or low level characters) since they can now use their spare move action to be stealthy or spot hiding enemies.

The iterative attack rules are actually taken from a post on another thread somewhere on the GITP 3.5 boards. The idea that it's almost required for a melee martial character to have some way to move and full attack in the same round is kind of odd to me, and buffing standard action attacks is a response to that. Now a high level build that can't do that still deal a respectable amount of damage, especially if it can also use it's swift action. Full attacks have also been buffed slightly by making 3rd and 4th iterative attacks have a decent chance of actually hitting.

The buff to critical hits is less broken than some might think. Critical hits don't deal that much more damage, especially compared to uber-chargers, and the dichotomy between purely legal 15-20 threat range Scimitars and grandfathered 3.0 Disciple of Dispater Lightning Mace Aptitude Kaorti Resin Scimitars with little in between is disappointing to me (note that Disciple of Dispater and using Aptitude with Lightning Mace isn't allowed in these rules). Critfishers are giving up some Strength to get the Dexterity for the Two Weapon Fighting line of feats plus must invest heavily in items and feats to buff the threat range and the attack rolls to make sure it hits, plus many creatures types are immune, plus magic items can boost defenses against critical hits, plus they're often tied down to a specific weapon or weapons. The ability to invest more resources to get a better result most of the time isn't what I would consider broken in this case. I'd take a good lockdown build over this any day, but it does provide an alternate way to deal damage.

The armor damage conversion and extension of negative HP both serve the purpose of making combat less of a fight to the death. Instead of only being staggered at exactly 0 HP and dying at -10 HP, meaning at mid to high level play one often goes from being fine to dead in a single attack, there's an area at which PCs and NPCs know to retreat and survive. Low level play is much more survivable (though not necessarily winnable), and mid to high level play becomes moderately safer. Damage conversion also makes in combat healing more powerful, since magical healing heals both lethal and nonlethal damage. In general, defeated enemies (and PCs) either flee or drop unconscious rather than have every fight be a fight to the death.

I really like the fear change too, it makes using fear more enjoyable for both DMs and PCs.

Dragon Magazine in the 3.5 era is generally allowed unless it's on the ban list, though certain things may be banned or changed depending on what it is. Splitting weapons are allowed, since archery is already somewhat underpowered in 3.5 compared to melee. Precision damage only applies once per initial arrow though.

The point buy based on LA is instead of missing levels, not in addition to. So a Goliath compared to an Orc has -2 DEX, +2 CON (fine depending on build), +2 to all mental stats (fine), movement stuff (okay), no darkvision but also no light sensitivity (fine), and powerful build and +2 to sense motive, plus different access to feats and prestige classes. So a Goliath might have stats 18/12/16/8/8/8 while the Orc has 21/14/14/6/6/6 if they focus on physical stats alone, which isn't that much of a difference. You can argue which has the better deal, but the idea that the higher the LA is, the fewer the viable classes is somewhat intentional. More bizarre creatures are closer to an archetype, while creatures closer to humans have more variety among their species. So for classes that require one or two high scores, a higher LA creature is better, whereas classes that require multiple high or medium scores are better suited for lower LA creatures.

The class tier system is based on the idea that higher tier classes tend to improve quadratically, whereas lower tier classes tend to improve linearly or are even frontloaded. Hence, that trend is reversed for feats and ability score increases, meaning the classes are roughly equal across levels. The problem with the system comes up when lower tier classes do improve quadratically (or at some other polynomial), making it weaker at low levels when it actually needs the boost but super powerful at higher levels when it doesn't need it. The Soulborn, Divine Mind, and Shadowcaster are probably the most egregious of this category. That said, let's compare the Fighter and Soulborn as this is a good example of when the system doesn't work, which I'm grateful to you for pointing out.
What does a high level Fighter look like? Generally it fits into one or more of three categories. First, a generalist. This Fighter has the basics of a charger build, and the basics of a lockdown build, and the bare minimum needed to ranged attack, can deal okay with concealed enemies, etc. They aren't particularly great at anything, but they can adapt to a fight based on the circumstances of the fight. Second, a specialist. This is where you get your dual wielding double hand crossbows, your AoO lockdown specialists, your parry specialist who takes all the parry feats including Incredible Parry enough times that they can block any attack against any of their allies, your dual wielding super critfisher builds, etc. Any build that's super feat intensive can be achieved fastest by a single class fighter, plus at higher levels they can finally diversify a bit. Third, a dipper. Since fighters can quickly can get a combat style or two under their belt fairly quickly, they can take a dip in other dip friendly classes without losing too much. They can take a level or two in martial adept classes, Incarnate or Totemist, or even a level in Warmage, Bard, Trickster Variant Spellthief, or Duskblade followed by Practiced Spellcaster, Obtain Familiar, and Improved Familiar and take the mounted combat tree plus the extra versatility from low level spells. It is fairly rare that anyone ever takes 20 levels in Fighter instead of enough levels to get the feats they need plus a dip to enhance their abilities. Plus they get Melee or Ranged Weapon Mastery and both good and bad ACFs, along with great weapon and armor proficiencies.
What does a high level Soulborn look like? Soulborn have a roughly linear progression for most class features, with proficiencies being front-loaded and essentia and chakra binds being back-loaded. If you look at the other Tier 5s, which apart from the Soulknife are all front-loaded, you can see why the quadratic feat and ability score progression is a problem for this particular class. However, I view the solution to this being moving it to Tier 4.5 rather than abandon the Tier system entirely. Meanwhile, let's look at it as being in Tier 5. At early levels, it's basically a fighter with fewer feats and an extra immunity. Once essentia comes online, it gains a ton of versatility, and is able to get one or two melee combos up in addition to soulmelds. Once you hit the later levels, you're getting Extra Chakra Bind enough times to bind all of the binds you've unlocked (I might want to weaken that feat) and have unlocked Incarnate and Totemist binds to aid your soulmeld versatility. You can even take Martial Study and Martial Stance, the Binding feats, and other small feat investments. Note that Bonus Essentia can be taken only once, so after that you need to take normal Incarnum feats to gain more essentia. Compared to an Incarnate, you have more Soulmelds and can use all Chakra Binds but fewer Essentia and slower chakra bind acquisition, Incarnum Defense instead of Incarnum Radiance, the feats and ability scores needed to specialize in one or more areas beyond just soulmelds, much better Fort but worse Will saves, better save DCs on your soulmelds, and some other stuff. Soulborn is still better by a fair bit, but not ridiculously so.
Comparing Fighter and Soulborn by level:
5th: A fighter has 6 feats, but has decent ACFs even at this level. A Soulborn has 5 feats, one of which must be an Incarnum feat, as well as one soulmeld, Smite Opposition, and Incarnum Defense. Depending on what build the Fighter is going for, the win probably goes to the Soulborn in a fight, and definitely goes to it in terms of versatility.
10th: A fighter has 14 feats, with some decent ACFs, and can get Melee or Ranged Weapon Mastery by this point. The Fighter has one or more melee combat builds online at this point and might have some form of decent range. If it took a one or more level dip in martial adept classes (or Binder plus Improved Binding, etc.) then that opens up a lot of in or out of combat versatility. The Soulborn has 12 feats, two of which must be Incarnum feats (and another two of which are realistically going to be Extra Chakra Bind), plus a variety of soulmelds (some of which are set in stone since they're from Shape Soulmeld), some chakra binds, okay essentia, and Smite and Incarnum Defense. The win still goes to the Incarnate, somewhat due to it having the feats for a melee combo in addition to its Incarnum abilities.
15th: A fighter has 22 feats, though it has likely given some of these up in exchange for a dip at this point. If not, it's going for an ultra specialized extremely feat intensive build. At this point the ability score disparity between the two classes is really starting to show itself, especially if the Fighter went for INT to get a lockdown build and the Soulborn didn't. A Soulborn also has 22 feats, but three are Incarnum feats. It has at point settled on a combat build incorporating the non-optional soulmelds from Shape Soulmeld and the six chakra binds it gets from the class and feats. I've ignored magic items until this point, but by 15th level characters have the ability to make up deficiencies through magic items, and Soulborns either have to take the Split Chakra feat or not use a magic item in a slot with a chakra bind. Even though the Soulborn looks obviously more powerful, many of its feats are used up to get soulmelds, get more essentia, get more chakra binds, get a melee combo, use magic items, etc. whereas the Fighter afford to take feat taxes for good feats, string together a bunch of feats working in unison, take dips for versatility, etc. Still goes to the Soulborn, but not at an insane scale.
20th: A fighter has 30 feats, though at this point some are given up for ACFs or dips. By 20th level a fighter has the feats and WBL to actually do a double hand crossbow machine gun build with Splitting and Force on both Crossbows and DEX to damage. But it also has the ability to sense hidden enemies decently, have CON to will saves and immunity to a bunch of things, and trip or stall any enemies that come within 30 feet. With 30 feats that aren't called for other than 11 being fighter feats there's a lot of stuff you can do. A Soulborn not only has 31 feats, three of which must be Incarnum feats, it also has tons of Chakra Binds, tons of soulmelds, decent essentia, one or two melee options, an okay ranged option, and much better ability scores. On the other hand, the problems with feats being called for has gotten even worse, and very few magic items to cover up any remaining deficiencies are usable. A Soulborn undoubtedly has the Fighter beat at this point, barring an severe disparity in optimization.
Let's see what happens when the Soulborn becomes part of Tier 4.5: 5th level has 4 feats, 10th level has 10 feats, 15th level has 17 feats, 20th level has 22 feats. This makes the fighter much more competitive since the Soulborn has to choose between keeping up with soulmelds, chakra binds, essentia, using magic items, and a decent melee combo. Thanks for pointing out this issue to me, and feel free to argue more in replies.

As for 2 level fighter dips (or generic warrior or expert or monk dips, or one level mariner dips) no longer being optimal in most cases, that was completely intentional. These dips give more feats early on at the cost of fewer feats later, and are most useful to upper tier that aren't losing ability increases or feats (or at least not as many). Instead of mid to high level low tier martial builds being composed of dips in a bunch of front-loaded classes, they can have a major class with possibly a dip or two to gain some versatility.
Also, Midnight Augmentation's limits to invested essentia, requiring essentia, only applying to one power, requiring expending psionic focus, and reducing by half a level's cost rather than a full level like Midnight Metamagic is the reason I don't think of it as broken and thus is perfectly fine to use in something like an Incarnate/Psychic Warrior build.

I think that covered most of people's concerns. If there's anything else you want to know about, just say so. I'll hopefully get back to faster than almost three weeks this time.