Since I noticed you had the Final Fantasy protagonists unworked, I decided to handle the one I obviously know, which would be Terra. You're free to debate, though do note - I take her very seriously (if not, just ask the guys at the FFRK thread).

Race: Human
Template: Half Fire Elemental (LA +3)
Starting Stats: Str 14, Dex 10 (14), Con 14, Int 8 (10), Wis 10, Cha 18 (20)
Starting Feat: Fire Bloodline (Dragon Compendium)

Spoiler: Progression table
Level Class Base Attack Bonus Fort Save Ref Save Will Save Skills Feats Class Features
1st – 3rd Half Fire Elemental +0 +0 +0 +0 -- -- Natural Armor +1, Innate Spellcasting
4th Half Fire Elemental/Fighter 1 +1 +2 +0 +0 Concentration 2 ranks, Spellcraft 2 ranks Block Arrow --
5th Half Fire Elemental/Fighter 1/Battle Sorcerer 1 +1 +2 +0 +2 Concentration 3 ranks, Spellcraft 3 ranks -- Metamagic Specialist (can cast spells without increasing casting time 3/day)
6th Half Fire Elemental/Fighter 1/Battle Sorcerer 2 +2 +2 +0 +3 Concentration 4 ranks, Spellcraft 4 ranks Feats Practiced Spellcaster (Battle Sorcerer)
7th Half Fire Elemental/Fighter 1/Battle Sorcerer 3 +3 +3 +1 +3 Concentration 5 ranks, Spellcraft 5 ranks -- --
8th Half Fire Elemental/Fighter 1/Battle Sorcerer 4 +4 +3 +1 +4 Concentration 6 ranks, Spellcraft 6 ranks -- --
9th Half Fire Elemental/Fighter 1/Battle Sorcerer 5 +4 +3 +1 +4 Concentration 7 ranks, Spellcraft 7 ranks Blistering Spell Domain Access (Healing)
10th Half Fire Elemental/Fighter 1/Battle Sorcerer 6 +5 +4 +2 +5 Concentration 8 ranks, Spellcraft 8 ranks -- --
11th Half Fire Elemental/Fighter 1/Battle Sorcerer 7 +6 +4 +2 +5 Concentration 9 ranks, Spellcraft 9 ranks -- --
ECL 12th -> ECL 11th (LA 3 -> LA 2)
11th Half Fire Elemental/Fighter 1/Battle Sorcerer 8 +7 +4 +2 +6 Concentration 10 ranks, Spellcraft 10 ranks Blistering Spell --
12th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1 +8 +6 +2 +7 Concentration 11 ranks, Spellcraft 11 ranks -- Ignore spell failure 10%
13th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 1 +9 +8 +2 +7 Concentration 12 ranks, Spellcraft 12 ranks 1 available feat --
14th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 2 +10 +9 +2 +7 Concentration 13 ranks, Spellcraft 13 ranks Searing Spell --
15th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 3 +11 +9 +3 +8 Concentration 14 ranks, Spellcraft 14 ranks -- --
16th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 4 +12 +10 +3 +8 Concentration 15 ranks, Spellcraft 15 ranks -- --
ECL 17th -> ECL 16th (LA 2 -> LA 1)
16th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 5 +13 +10 +3 +8 Concentration 16 ranks, Spellcraft 16 ranks Twin Spell --
17th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 6 +14 +11 +4 +9 Concentration 17 ranks, Spellcraft 17 ranks -- --
18th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 7 +15 +11 +4 +9 Concentration 18 ranks, Spellcraft 18 ranks -- --
ECL 19th -> ECL 18th (LA 1 -> LA 0)
18th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 8 +16 +12 +4 +9 Concentration 19 ranks, Spellcraft 19 ranks Quicken Spell --
19th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 9 +17 +12 +5 +10 Concentration 20 ranks, Spellcraft 20 ranks --
20th Half Fire Elemental/Fighter 1/Battle Sorcerer 8/Spellsword 1/Eldritch Knight 10 +18 +13 +5 +10 Concentration 21, Spellcraft 21 -- --

Spoiler: Spells per day/Spells Known
Spells per Day/Spells Known
Level 0lvl 1st 2nd 3rd 4th 5th 6th 7th 8th 9th
1st - - - - - - - - - -
2nd 4/3 2/1 - - - - - - - -
3rd 5/4 3/1 - - - - - - - -
4th 5/4 4/2 - - - - - - - -
5th 5/5 5/2 2/1 - - - - - - -
6th 5/5 5/2+1 3/1+1 - - - - - - -
7th 5/6 5/2+1 4/1+1 2/1+1 - - - - - -
8th 5/6 5/3+1 5/1+1 3/1+1 - - - - - -
9th 5/7 5/3+1 5/1+1 4/1+1 2/1+1 - - - - -
10th 5/7 5/3+1 5/2+1 5/2+1 3/1+1 - - - - -
11th 5/7 5/3+1 5/2+1 5/2+1 3/1+1 - - - - -
12th 5/8 5/3+1 5/2+1 5/2+1 4/1+1 2/1+1 - - - -
13th 5/8 5/3+1 5/3+1 5/3+1 5/2+1 3/1+1 - - - -
14th 5/8 5/3+1 5/3+1 5/3+1 5/2+1 4/1+1 2/1+1 - - -
15th 5/8 5/3+1 5/3+1 5/3+1 5/3+1 5/2+1 3/1+1 - - -
16th 5/8 5/3+1 5/3+1 5/3+1 5/3+1 5/2+1 3/1+1 2/1+1 - -
17th 5/8 5/3+1 5/3+1 5/3+1 5/3+1 5/3+1 4/2+1 3/1+1 - -
18th 5/8 5/3+1 5/3+1 5/3+1 5/3+1 5/3+1 5/2+1 4/1+1 2/1+1 -
19th 5/8 5/3+1 5/3+1 5/3+1 5/3+1 5/3+1 5/2+1 5/2+1 3/1+1 -
20th 5/8 5/3+1 5/3+1 5/3+1 5/3+1 5/3+1 5/2+1 5/2+1 4/1+1 2/1+1

Spell List:
0 – acid splash, daze, detect magic, detect poison, light, message, resistance, touch of fatigue
1st – burning hands, cure light woundsD, hypnotismF, lesser orb of fire, summon monster I
2nd – combust, cure moderate woundsD, pyrotechnicsF, resist energy, scorching ray
3rd – cure serious woundsD, dispel magic, fireball, tonguesF, vampiric touch
4th – cure critical woundsD, dimension door, fire shieldF,orb of fire, polymorph
5th—arcane fusion, break enchantment, cloudkillF, mass cure light woundsD, teleport
6th—flesh to stone, greater dispel magic, healD, summon monster VIF (fire creatures only)
7th – arcane spellsurge, delayed blast fireballF, regenerateD,reverse gravity
8th – incendiary cloud, mass cure critical woundsD, sunburstF
9th – gate, mass healD, meteor swarmF

Spoiler: Justification
The biggest challenge, from the start, is how to work with her race (half-Esper). The "half" part would suggest a template, though it could also suggest a race (see: Half-Elf, Half-Orc). I decided for an existing template to make things easier (and somewhat more legal), and I ended up with Half-Elemental (Fire), as it fits several traits - she specializes in Fire magic above anything else, and the template grants a plethora of SLAs related to fire, which works. Not only that, she gets a few boosts, most notably to Dexterity, Intelligence and Charisma, which leads to the second point.

Then, classes. I took one level of Fighter to qualify for Eldritch Knight, as she's a gish focused on spellcasting (and blasting, mostly). This gives her proficiency with her usual weapons (daggers, swords, also flails as all Imperial characters are proficient in them), all kinds of armor (including heavy armor; canonically, she can wear the heaviest armor available) and shields, covering her fighting side. The feat is an afterthought, but it could easily be Combat Casting (you'll see why soon). Then, eight levels of Battle Sorcerer...why, you ask? Battle Sorcerer sacrifices some of her spellcasting ability (which is already hindered by the loss of 1 spellcasting level) for more fighting ability, ending up with cleric BAB, a better HD (d8) and redundant proficiencies. The big loss is in terms of spells known, as she makes another sacrifice later on, but she ends up with roughly the same amount of spells known thanks to the Fire Bloodline feat (from Dragon Compendium; sure, it's frowned upon, but Dragon Compendium is technically 1st party content AND fitting) and the Domain Access ACF from Complete Champion. There's a reason for the choice, which I'll explain later on. A dip in Spellsword allowed me to further boost her skills and give her the ability to ignore some of the spell failure from heavier armor, meaning she could equip a Mithral Breastplate, or even Mithral Twilight Full Plate, and be capable of casting spells with virtually no ASF. That's a huge plus. Finally, even if it means the loss of yet another spell level, she goes full Eldritch Knight. That leaves her with 9th level spells and BAB over 16, which makes her a gish proper.

Feat-wise, Fire Bloodline adds a few interesting spells. Hypnotism and Tongues definitely don't fit, but spells like Delayed Blast Fireball and Fire Shield do. The main reason I do that is because of the Sunburst spell, which I equate with the Holy spell from the FF series, though Holy is supposed to be the strongest White Magic spell, so it technically could count as an Epic spell. Because of the Fighter level and the Eldritch Knight level, Terra gets two spells that can aid her in combat, though her focus is on magic, so they're mostly solid filler (ideas are welcome!) That said, the choice of metamagic is interesting, as it makes her an undisputed Fire specialist, what with increasing the damage of Fire spells AND make them pretty much irresistible to all but creatures that absorb the energy type (though it ignores the regional prerequisite). Twin Spell and Quicken Spell are feats I chose because of her appearances in later games, where she's given the ability to Doublecast (Dissidia, Record Keeper, eventually in Brave Exvius) as befitting of a Red Mage, which is closer to her actual class (in essence, she's a Red Mage on steroids, as she can equip better armor and cast stronger spells).

The spells were another problem, but they were mostly solved aside from three spells. She knows a handful of healing spells, which are dealt with the Healing domain as part of the Domain Access ACF. Her fire specialization is evidently dealt with, and some of her odd spells (Drain, Break, Graviga) are dealt with similar spells (Vampiric Touch, Flesh to Stone, Reverse Gravity). The three spells that I couldn't work with were Raise/Arise (Sorcerers can't cast Raise Dead, and there's no domain that grants such), Meltdown (the closest spell I could think was Fire Storm, and that would have most likely required access to the Fire domain; the slot is filled with Incendiary Cloud instead) and Poisona (because Sorcerers can't cast Neutralize Poison, either). Dispel was also easy to deal with, and she can handle that task quite well (both sources of Dispel Magic + Break Enchantment for allies). As for Ultima? That's for three levels later, when she achieves 24 ranks in Spellcraft and gains the Epic Spellcasting feat - there's no doubt that Ultima IS an Epic spell, judging by how the game treats it.

There are a few filler choices, though. Polymorph is there as a homage to her Trance ability, though you can't really turn into an elemental by means of that spell. Resist Energy isn't a spell that would exist on the FFVI world (it's part of latter spells, specifically the Bar[Element] line of spells), but it's a good filler spell. Finally, Gate is there as part of her link to Espers, as well as being the one who opened the Gate to the Esper World, so you'd expect her to be able to depart to her birthplace if necessary. Arcane Fusion, Greater Arcane Fusion and Arcane Spellsurge are other ways to mimic Doublecast, further reinforcing her spellcasting ability in the same way you'd boost a Red Mage.

I declined giving her equipment because the best equipment in FFVI is so specific; the Ultima Weapon is essentially a Weapon of Legacy, the Ragnarok is essentially an intelligent weapon, the Minerva Bustier would qualify as an Epic weapon, and accessories as they stand blur the line, so assume she holds a sword, a breastplate, maybe a shield, some sort of magic headgear (her ribbon is a good start!), a Cloak of Charisma/Cloak of Resistance (her cape), a dagger, and maybe one or two more magic items (her iconic Pendant, and maybe some boots). I really don't deal much with equipment, since translating FF equipment to D&D stats usually doesn't work as intended, in particular the weapon that fits her the most (Enhancer, which is meant to enhance magic power).

Finally - her stats are meant to reinforce her skill as a warrior and her power as a spellcaster. That is why her Charisma is so high, but she has good physical stats overall. Her Intelligence and Wisdom are low, but not very low (they're actually non-heroic average). Her low Wisdom reflects her ignorance about the world (due to her amnesia and her upbringing) but also justifies why she was mind-controlled (her Will save sucked; luckily, it gets better later on once she gets the level of Spellsword). I wish I could say the same for Intelligence, but...well, she's more heart than anything else. You could justify moving 2 points from Dexterity to Intelligence if you want. Her skills are Concentration (she's a warrior-mage, after all) and Spellcraft (knowledge specific to spells); the third skill is left open, though she does make a decent rider. If you're aware of the DragonMech 3rd party campaign setting, she could have her first level of Fighter replaced by Mech Jockey and have her skill points as Human spent in Mech Piloting, as a nod to her skills as a Magitek Armor user. Creating the Magitek Armor, specifically her variant that's more powerful than the norm, would be an interesting challenge.