Final Fantasy IV
I would have taken out Yang and put in Rosa + Rydia for the "original 5". Not to mention there's a lot more story synergy with those 5 together.
Final Fantasy VI
Honestly, I would have taken out Shadow and put in General Leo. I do like Shadow, but I think General Leo would have a lot more interesting implications with Terra and Kefka.
Final Fantasy VII
Barret would have been a cool alternative to Yuffie really. Actually if anything, I'm shocked they didn't use Vincent.
Final Fantasy VIII
I understand why Seifer's in there but... I don't know. Rinoa would have rounded out this selection a lot more I think.
Final Fantasy IX
No Garnet OR Beatrix? SMH.
Final Fantasy XI
Why didn't they include Prishe actually? How odd.
Ever since Shantotto had been in Dissidia, I always imagined a "party" being a selectable character. Basically you'd have the Hume be the leader, with an Elvaan, Galka, Tarutaru and Mithra being part of the attacks (kind of like Yuna's playstyle). You could even have them equipped like the Ark Angels as a throwback (WAR, PLD, SAM, BLM, BST). As for the characterization, you could very easily use the whole storyline behind each race... I DUNNO. I think this would have been a lot of fun.
Final Fantasy XII
Ah yes... the "youngster inserts". No Balthier, Fran, Ashe or Basch is just travesty really. Even just one of those 4 would have been nice.
Final Fantasy XIII
Vanille would have been a good addition here too.
Final Fantasy Tactics
I'm super glad Ramza was added at all, but c'mon- we need Delita too OBVIOUSLY.
My 2 cents.