Here is mine:

Good/Bad

Red Mage/Astos
Maria/ Leon
Desh/ Xande ( they donīt ever meet so this pair up might not work)
Golbez/ Zemus
Faris/ Magissa ( that bitch who shoots poison arrow into Lenna and summons her husband )
Leon/Gestahl ( I think it would cool if everybodys favorite guest was playable )
Barret/ Dyne (every game needs black man with a gun arm)
Zell/Biggs (Just like someone said)
Freya/Beatrix
Kimahri/ Seymor
Ashe/Vayne

And Mystic Quest special with Tristam and Dark King.