I'd probably give the people of Cocoon some redeeming qualities besides being hateful, xenophobic morons who I WANT to die. And give the fal'Cie an actual plan rather than just "Do stuff and hope Orphan ends up dead"

I'd also remove Fang's six seconds of mutiny. Oh, sorry, twelve, forgot she does it again on Pulse. -.-

Maybe I'd have Vanille get killed by one of the many people who rightly want to do so by the end of the game for royally screwing them over so much.

I'd give more substance to the eidolons. What are they? Do they fal'Cie assign them? Are they fal'Cie sympathetic to the l'Cie plight? Random monsters that operate in a Pokemon "beat me up, I'll be your friend" mentality? What?

I would change it so that the party doesn't fight Oprah for no reason, knowing that doing so would be the certain death of everyone and just kinda banking on a Deus Ex Machina popping out of nowhere to save them. Maybe one of your party members as Ragnarok would have made a good boss, you get to choose which one and the ending changes accordingly.