Godlike
Arceus (Pokémon) v Ferham (Mega Man X: Command Mission): This might need greater analysis, but... Cosmic Power is spoiled by the fact that Ferham can freeze Arceus, then use Crimson Shade and start launching critical hits and such. Freeze also cancels any resistances a target may have, to boot. EDIT: Wait, Ice Plate. That cripples Arceus' own damage, but does give him a better shot due to freeze immunity... still, kneejerking he's too vulnerable to a good physical blitz then.
Oz (The Wizard of Oz: Beyond the Yellow Brick Road) v Ghaleon (Lunar: Silver Star Story Complete): Uh. Um. Yeah I need to sort out how I view Oz. Damnit CK why do you enjoy using the least rankable characters from games.
Altima (Laggy Fantasy Tactics) v Xorn (Grandia III): Thinking the wall phase gives her the edge she needs in a fast slugfest like this. Helps that Xorn hits her wrong defence.
Archibald Grims (Super Robot Taisen Original Generation 2) v Empyrea (Dragon Quest VIII: Journey of the Cursed King): My view of SRW bosses makes them extremely mediocre against those with uncounterable damage. Unfortunately for Empyrea, all she has there is a OPR Zap which scares nothing. Instead she has to use her physical attacks, which provoke evil, evil, 150 Will Attacker/Revenge/whatever the hell Archibald had that made his damage so gross, and she has to provoke them twice a round! Yeaaah, no.
Heavy
Citrine (Xenosaga: Also Sprach Zarathustra) v Grand Maestro Mohs (Tales of the Abyss): Oh god, Citrine isn't very good, but she at least belongs in the division. Mohs is a Middle against mages and a Light against physical attackers. Barely half the HP of Largo/Legretta coupled with lol defence and bad damage... yeah what the fuck.
Ancel (Valkyrie Profile: Covenant of the Plume) v Lucian (Valkyrie Profile): Good fight, but it does feel clearly Lucian's? Ancel has an initiative tiebreak (bad move/range) working against him, and Lucian's damage is probably high enough to maintain his 2HKO here.
Middle
Lion (The Wizard of Oz: Beyond the Yellow Brick Road) v Pesmerga (Suikoden Series): Pesmerga's high pdur reduces Lion damage to a 4RKO, but Half-Life brings that back to a 3RKO. Lion has just enough pdur to stave off a 3HKO and goes first. D-Formation can only tilt things further in Lion's favour.
Lieselotte (Valkyrie Profile: Covenant of the Plume) v Kesaran Pasaran (Wild ARMs 4): Not sure which form of Liese I vote on, never mind how either does here.
Niccolo (Legend of Mana) v Tifa Lockheart (Final Fantasy VII): Niccolo in Middle? I dunno about that.
Light
Lyre (Fire Emblem: Radiant Dawn) v Pidgeot (Pokémon): ... pretty sure.
Ellen (Fire Emblem: Sword of Seals) v Healie (Dragon Quest IV): ... also pretty sure.
Luigi (Mario & Luigi Series) v Raijin (Final Fantasy VIII): Luigi was a pretty wretched dueller IIRC, Mario seemed better in almost every meaningful stat.