Hmm...let's see...

FFI: Thief, Red Mage, Black Mage, White Mage, Monk (Heroes) and Lich, Marilith, Kraken and Tiamat (Villains). It's asking for too much, but it's the thing that makes most sense. Any pair would be fine, although I'd incline for Red Mage and Marilith for main choices. Red Mage would reinforce Cosmos' imbalance towards Magic (even though Onion Knight as Sage, Terra and Shantotto are potent magicians, there's still a need for a tad more magic). Marilith, along with Lich, is the most human (so to speak) of the Fiends, and an interesting addition.

FF2: Hard to pin. Gordon for the good guys and Leonhart for the bad guys is a pretty solid choice. Though, I'd go with Min-wu: he's the first of the White Mages. Or Josef. Or even Ricard, but it would conflict with Kain. However, there is little reason not to think Leon is the definite choice for Chaos' side; heck, it would be awesome to have Cecil fight Leon...

FF3: Desch's story is heartwarming, but I'll throw the Wild Card in here: Do(r)ga and Unne(i). Dorga as master of Time, and Unne as mistress of Dreams, both allies of the heroes and forced to fight them.

FF4: I'd gladly comply with Kain and Zemus, but I have one that, despite the lack of popularity, would be one I'd definitely love to see: Edge vs. Rubicante. Rubicante would be a tad reluctant to be on Chaos' side, and perhaps would incline towards the Emperor's side, but he'd be an interesting choice much on the line of Cecil's dual-job style (except his would be dual-element). Edge, on the other hand...might need some workout, but thematically it fits Rubicante. However, no complains for Kain vs. Zemus.

FF5: Hands down, Galuf. A big salute to the old man. As for opponent...I'd go wild and say Magissa. She had a really short time in the spotlight, but her battle was, little to say, interesting.

FF6: Tough choice here. Popularity says either Edgar or Locke for heroes, and definitely Gestahl as a villain. However, if we're going to be reviving dead people, might as well throw a bone to good ol' Leo. It would be very interesting, to see Leo facing someone whom he despises despite being on the same "team" (Kefka) and against his own liege (Gestahl).

FF7: Really difficult choice. Zack would be a decent choice, but it would be mostly a palette swap of Cloud (except for Omnislash, but using the DMW system as an EX Mode). Vincent seems the obvious choice. Pretty obvious choice; EX Mode being Chaos (or him using Death Penalty). As for a villain...again, a tough choice, given that the Turks could use some love.

FF8: Heroes have a tough one here. But, given a read not so long ago, I'd go Rinoa vs. Seifer. Failing that, Laguna vs. Adel.

FF9: Hmm...Brahne? No...not enough to justify being on Cosmos' side. If I were to choose, I'd have Beatrix be the hero choice, but I must relinquish and accept she could do a magnificent villain; the kind that accepts commands without question (even if those are orders against her own way of being), but that slowly shifts loyalties elsewhere. As for the hero choice....STEINER. Ol' Rusty needs some love...

FF10: Yuna and Seymour. I know Auron is an appropriate choice, but the entire idea was that if Seymour was to get in, Yuna had to enter. Not a difficult choice. Though...just for knacks, I'd make her Gunner Yuna, and her EX Mode being High Summoner Yuna (and alternate version Yuna being Songstress Yuna); Seymour would have either Natus or Omnis as his EX Mode.

FF11: To complete, I'd say...Shadow Lord. I honestly though Shadow Lord was going to be there. But, if I were to do something out of the way... Ma'at. Yeah, the guy that raises the level cap of your heroes.

FF12: Either Balthier or Basch. I have no complaints for either of them.

If I could add one other FF, even if it's not one of the Final Fantasy main games: FF Tactics. Ramza and Delita. I feel that they could have done a nice story with them, what with the Zodiac Stones (as part of their world's crystals), their old friendship, Delita's on-off way of being a villain and Ramza's idealism constantly marred by circumstances. EX Modes for both would be quite hard, however.