Protagonist
Sonic vs Mario
Charizard vs Blastoise
Reshiram vs Zekrom
Pokemon Trainer Red vs Pokemon Trainer Blue
Fox McCloud vs Wolf O'Donnell
Banjo vs Gruntilda Winkybunion
Ness vs Porky(Pokey) Minch
Samus vs Ridley
Captain Falcon vs Samurai Goroh
Bayonetta vs Jeanne
You can tell just from this current list than all my noms are very Nintendo/SEGA driven. I considered NiGHTS vs Reala and The Knight vs Tim(hehe). Maybe the former can be done via a certain fan site.