Cain and Gilgamesh, hands down. I've got my own dream roster for a sequel mostly worked out:
FFI - Warrior of Light, Garland, Red Mage, Chronodia
FFII - Frioniel, The Emperor, Leonheart, Deumion
FFIII - Onion Knight, Cloud of Darkness, Doga, Xande
FFIV - Cecil Harvey, Golbeza, Cain Highwind, Zemus
FFV - Butz Klauser, Exdeath, Faris Scherwiz, Gilgamesh
FFVI - Tina Branford, Cefca Palazzo, Lock Cole, Leo Cristophe
FFVII - Cloud Strife, Sephiroth, Zack Fair, Genesis
FFVIII - Squall Leonheart, Ultimecia, Laguna Loire, Seifer Almasy
FFIX - Zidane Tribal, Kuja, Adelbert Steiner, Beatrix
FFX - Tidus, Jecht, Yuna, Seymour Guado
FFXI - Shantotto, Kam'lanaut
FFXII - Basch fon Ronsenburg, Judge Gabranth
FFXIII - Lightning, Noctis Lucis Caelum
FFI, without Chaos and Garland, Chronodia is really the only unique enemy left, and she could be pretty cool as a major villain.
FFII, none of the lead characters are really that unique or would have good EX Modes, and most of the villains aren't that cool, but Deumion is interesting and could have good interactions with several other villains and characters, being the guardian of the strongest magic. Phyrekos EX Mode.
FFIII, Xande is a no-brainer, but Doga is just a filler spot.
FFIV, no brainers.
FFV, also no brainers.
FFVI, Leo might be a stretch, but Geshtal never did anything. Celes instead, maybe.
FFVII, tough one, mostly due to lacking notable villain material. Vincent and Hojo? Tifa and... Rufus? Barret and Dyne? Ehh to all of them.
FFVIII, Laguna would be pretty interesting, but there could be other choices.
FFIX, not many villains and Garland is a no go, so Beatrix. Steiner is, therefor, a no-brainer, no pun intended.
FFX, no brainers.
FFXI, Kam'lanaut looks cooler, but his brother could probably work just as well. Kam'lanaut has clear normal/EX Mode designs, though.
FFXII, Balthier could work, but Basch as Gabranth's rival works better.
FFXIII, no brainers.