Personally I would have included the following:

1) About 30 more minutes of characters interacting intserspersed between the fight scenes. The fight scenes were nice eye candy, but the character interactions are at least half of what made the game great in the first place.

2) A little more complexity in the villains. Especially Loz and Yazoo. I would have written a scene where Marlene speaks with Loz and finds that they actually have something in common (a lost mother). Also I would have the villains actually care about the orphan children, even just a little.

BTW, if you really want to see a chocobo race animated, watch Last Exile. There's an episode that should have been titled Gold Saucer.