My biggest gripes with the game would be...

1. The difficulty in getting gil late in the game, particularly given how much you need in order to achieve all trophies. I need to get 61 more Platinum Ingots. I expect to spend days on end doing this. =/ At least it's a goal, I guess, but they could have made a better way to do it or at lease have the Gui drop Ingots more often or even something more valuable.
2. The lack of minigames in the 'City of Dreams'.
3. The rather confusing ending.
4. The late, late, late party selection option. I can't remember for certain, but I think even when you have four characters, you still can't switch them around.
5. Chapter 10's designfail.

There's probably more, just can't think of them right now.