Divine Beings
Kefka Palazzo (Final Fantasy VI) vs Nyarlathotep (Persona 2) - Kefka's one of the few characters who actually has "Destroyed the World" on resume, not to mention doing it while people were actively trying to stop him and getting to see it happen on-screen and not in flashback. That's enough to beat Nyarlie's rumors-become-true powers.
Vergil (SaGa Frontier) vs Ultimecia (Final Fantasy VIII) - Following my logic with Kefka here, Ultimecia actually manages to start compressing time and space down to a single point on-screen, whereas Vergil's nigh-immortality is about all we see him display of his powers.
Lenneth Valkyrie (Valkyrie Profile Series) vs Archangel Flonne (Disgaea 4: A Promise Unforgotten) - Well, at least Flonne has a giant robot. I will sum up all arguments on this match now: "Creation Goddess..."
Ashunera (Fire Emblem: Radiant Dawn) vs Cthulhu (Cthulhu Saves the World) - Petrify the World just slightly beats out Insanify the World.
Superhumans
Tir McDohl (Suikoden) vs Yuri Hyuga (Shadow Hearts Series) - True Rune bearers probably belong with Deities to me. Admittedly, so does Yuri, but Tir spoils most mortals.
T260G (SaGa Frontier) vs Katrina Lianne Elesius (Wild ARMs XF) - Awaiting arguments.
Belial (Wild ARMs 4) vs Vayne Aurelius (Mana Khemia: Alchemists of Al-Revis) - Oh crap, this is a damn good matchup. Vayne's power as a manufactured Mana of Wishing is apparently pretty hard for him to control and use offensively, but it's shown several times throughout the game to activate when he's under duress. Belial's powers of locking him in a pocket dimension are pretty much tailor-made for giving him the right amount of fear, danger, and time to cause him to wish himself out to safety. I think, ultimately, Belial has more control over her powers, but Vayne may survive long enough to... I dunno get her to fall for him? He seems pretty good at it in his home game, and Belial does seem to have that co-dependent personality that would for someone like him. This is a weird match up of tropes. Even ignoring tropes, he's a powerful enough fighter and alchemist that simply negating Belial's main trick with his Wishing powers is enough for him to overpower her. Awaiting other arguments.
Altima (Final Fantasy Tactics) vs Aya Brea (Parasite Eve) - Aya has no problems killing angels, but she might hesitate to kill a little girl while Altima's possessing her.
Warriors
Magdalen Harts (Wild ARMs: Alter Code F) vs Delita Hyral (Final Fantasy Tactics) - Magdalen is too honorable to handle Delita.
Flay Gunnar (Mana Khemia Series) vs Cliff Fittir (Star Ocean: Till the End of Time) - Match invalid, they are the same person.
Karel (Fire Emblem Series) vs Raquel Applegate (Wild ARMs 4) - my argument boils down to "Raquel's handled worse."
Squall Leonhart (Final Fantasy VIII) vs Aelia (Valkyrie Profile) - Again, not inclined to give Einherjar any special deity consideration since they aren't as special in-game as they are in-mythology, but Aelia has that neat Dragon trick. Squall is definitely a contender, but I generally kneejerk him as a pretty typical human while Aelia feels like she could play in Superhuman.
Civilians
Ryogo Kusama (Front Mission 3) vs Gina (SaGa Frontier) - I don't know FM3, but I'm voting Gina because she becomes one of Asellus' queens in the demon ending, and WhiteRose/LionPrincess/Rei are at least Warrior-level.
Ryotaro Dojima (Persona 4) vs Anastasia Romanov (Shadow Hearts: Covenant) - Even assuming Anastasia didn't have her camera, Dojima is not attacking anyone who is that close to Nanako's age.
Edward Chris von Muir (Final Fantasy IV) vs Arnaud G. Vasquez (Wild ARMs 4) - Pays him off. Arnaud is basically a mercenary and the stakes of this fight aren't so dire that Arnaud has any reason not to just throw the fight.
Nanako Dojima (Persona 4) vs Tengaar (Suikoden Series) - Tengaar might be willing to punish Nanako? But then, Nanako would have to have done something wrong to warrant it. In the end, Tengaar's not going to hurt a little girl.