Time for an all-girls hero line-up!

FF1:
Hero: Tricky one. Maybe a female Red Mage?
Villain: Like everyone else said, Astos.

FF2:
Hero: Maria, long range magic type
Villain: Leon. Duh.

FF3:
Hero: Female Onion Knight?
Villain: Xande. Again, a shoe-in.

FF4:
Hero: Rosa, utilizing her bow and holy magic
Villain: Kain, in all his brainwashed glory.

FF5:
Hero: Faris. Because crossdressers are awesome.
Villain: Gilgamesh. No question.

FF6:
Hero: Celes, with magic and a sword.
Villain: Gestahl, I guess. Not really sure but, whatever.

FF7:
Hero: Either Aeris or Tifa. Aeris for magic, Tifa for fisticuffs.
Villain: For Aeris, either Hojo or Jenova. For Tifa, maybe Rufus? Someone from Shinra anyway.

FF8:
Hero: Rinoa, with her frisbee and Sorceress powers.
Villain: Either Seifer being a carbon copy of Squall, or posessed!Edea as a carbon copy of Ultimecia.

FF9:
Hero: Garnet's the best candidate, definitely.
Villain: Either Beatrix or Garland, although two Garlands might be confusing.

FF10:
Hero: Yuna. Although I don't see how her role as Summoner/white mage could work...
Villain: Seymour. Because he's Yuna's villain.

FF10-2:
Hero: Here I personally think Yuna could shine the most. Her Gunner dressphere is much more combat-orientated than her FF10 incarnation.
Villain: Shuyin. Tidus redux.

FF12:
Hero: Ashe. Obviously.
Villain: At first I thought Vayne, but personality-wise he really doesn't fit with the 'destroy the world' theme the rest of the Chaos warriors have got. So maybe Rasler'sGhost!Occuria? It would be interesting, though a bit of a stretch...

FF13:
Hero: Lightning. Oh yeah.
Villain: Dysley I guess. Although he is kinda pathetic. Someone up above suggested Cid, but he's really more of Snow's villain.