Sounds like great idea!
As to your first question, Xavier, my vote goes for "a" option -
a) make it BG2/FFVIII style - using the BG2 engine, but in the techno-fantasy setting of FFVIII.
As Nanobyte said, there are prestige classes, but could they be really
prestige? I mean classes that are not available during generation, but can be accessed through quests/approp.lvl/etc.?
Also, may I ask whether a gamer would be able to create his own character for the game? (For me the main disadvantage of FF is that you have to play with a pre-maid character, not being able to choose race/gender/class/abilities/whatever).
Well, I'm afraid I have too many ideas, so I'll just stop talking for now

Anyway, best of luck with this project!
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Tanda,
with best regards from Guild of Assassins