I think it was a good idea to have all the main characters and main villains... It's more organized that way, for one.
blaugh Mostly, though... Well, not having played it, I don't know much about the story, but they've all got their counterparts on the opposite side. So... if, for example, they put Vincent? We'd have to have Hojo or something.
...Although I think it would have been cool to have
Yuna and
Seymour, maybe, instead of Tidus and Jecht... Their dynamic is just as good, maybe even better, and I really love Yuna. It would be nice to have another girl, too. So long as it's X!Yuna.
And, well, just for fun? Characters I would have liked to play as disregarding whether or not including them would ruin the game...?
Laguna! Stick a character with a machine gun in there; that'll be fun! Plus, Laguna's just awesome. Him or
Irvine, I'd be equally happy with either. Also,
Red XIII, 'cause it would be really fun to play as a quadruped.