Godlike
Loki (Valkyrie Profile) vs GenocideHeart (SaGa Frontier) - Kneejerk is that Loki just continues to OHKO each of GH's forms?
Ryu (Breath of Fire III) vs TimeLord (Saga Frontier) - Beating Ryu3 the only way people know how~
Heavy
Jeremy Non (Wild ARMs 4) vs Kiryl (Dragon Quest IV) - Jeremy probably heal-locks if he doesn't outright kill.
Time Mage (Final Fantasy V) vs Arnaud G. Vasquez (Wild ARMs 4)
Middle
Albel Nox (Star Ocean: Till the End of Time) vs Rudy Roughknight (Wild ARMs) - Faster and status-y-er.
Snow Villiers (Final Fantasy XIII) vs Lightning Farron (Final Fantasy XIII) - I think someone mathed this out before?
Light
Riki (SaGa Frontier) vs Lucia (Shadow Hearts: Covenant) - This is sad. Generally thinking that Riki has more durability and the healing makes it easier. I even allow Lucia some plot Crests, but I don't think it saves her here.
Fiona (Fire Emblem: Radiant Dawn) vs Vinsfeld Rhadamanthus (Wild ARMs 2) - Fiona = Imbue hype!
Ranking Data Mining:
FF4-2: The After Years... For all that it's terrible and it should feel terrible, there's some interesting character builds in there and it's probably got enough voters?
Legend of Mana: Has voters and fans and a stat topic that does a pretty good job of interpreting it. I'm just curious where it stands.
Other ideas that come to mind: ToV, ToGf, Dis4, LO, XB, Atelier Iris 1, AT1, FFMQ, LoH:Trails, VPDS, Tierkreis, SoD, WoZ, KHBBS