Difficult to say, because I feel every single Final Fantasy had unrealized potential. However, I'm gonna go with Final Fantasy X-2.
I'm surprised this hasn't been mentioned yet. The job system is great, but could've been better. I think the option to put monsters in your party (in the International version), training their stats and having them learn unique abilities is a great concept that had the unfortunate side-effect of making the game way too easy, because the monsters were just too strong.
Also, the whole idea of the whole world being open and almost everything being visitable at any point during the game is interesting, but there was so much that could've been improved. To sum things up, everything in this game could've been so much better.