Divine Beings
Arek the Absolute (Lufia Series) vs Kefka Palazzo (Final Fantasy VI) - My general feelings here are "while Arek may control Sinistrals, Kefka shows he can destroy things by getting his own hands dirty."
Althena (Lunar Series) vs Nyarlathotep (Persona 2) - No contest really, Althena's pretty low-tier for a True Deity, she gets smacked around by mortals all the time. Nyarlie may depend on the darkness/fear-of-death/whatever in humans' hearts to exist, but he's pretty good at manipulating humans when he wants to subtle, and plenty good at just blowing shit up when he's not.
Vergil (SaGa Frontier) vs Izanami (Persona 4) - I think Vergil is actually more of a superbeing, but considering that even normal people in SaGa Frontier seem to fit into that category, it makes sense that Vergil's up here. Even when you beat him in-game, he just keeps regenerating or something, so I'm going with nigh-unkillable-ness over Izanami's more vague powers.
Ryu (Breath of Fire: Dragon Quarter) vs Ultimecia (Final Fantasy VIII) - I haven't beaten BoF5, so I could be swayed, but I recall that Ryu using his full power outright kills him, so that's a bit of a limitation there that Ulti doesn't worry about. I'd also give her Griever credit and potential credit for any effects that Time Kompression might have on Ryu.
Lenneth Valkyrie (Valkyrie Profile Series) vs Gig (Soul Nomad & The World Eaters) - Lenneth makes Worlds, Gig eats them. Technically Lenneth should never run out of juice to keep up this cycle, but Gig's powers specifically increase the more things he has to consume, so eventually Infinity + Infinity beats regular old Infinity.
Laharl (Disgaea Series) vs Seraphim Flonne (Disgaea 4: A Promise Unforgotten) - Oh, you jerk, Hatbot. Even as a Seraphim, Laharl is canonically more powerful than Flonne in the NIS universe. There's a level chart and everything! Go meta-ness! (Admittedly, Random makes a good point about Flonne knowing Laharl's biggest weakness.)
Valmar (Grandia II) vs Ashunera (Fire Emblem: Radiant Dawn) - While Valmar was split up into multiple parts, Ashunera was split up into only two. The parts seem to have comparable power levels - Valmar pieces take hosts, can be beaten by humans, etc. Yune takes a host, Ashera can be beaten by humans, etc. I'm gonna go with "More parts likely equals more power when combined, given the parts are roughly equal."
Arceus (Pokémon) vs Cthulhu (Cthulhu Saves the World) - Slightly less easy to capture!
Superhumans
Stocke (Radiant Historia) vs Tir McDohl (Suikoden) - Hmm.. Spy with the power over Time, and a General with the power over Death. Good match-up. Overall, I think Stocke demonstrates better control over his abilities, so he probably gets the upper hand here.
Dhoulmagus (Dragon Quest VIII: Journey of the Cursed King) vs Yuri Hyuga (Shadow Hearts Series) - Yuri gets Amon at the very least, which is already a match for Dhoulmagus at his peak. If you give Yuri Seraphic Radiance, or take into account that he's defeated actual -Gods-, it's not really that close.
T260G (SaGa Frontier) vs Bowser (Mario & Luigi: Bowser's Inside Story) - If you allow Giga Bowser, then T260G gets her form as the core of a giant spaceship, which evens the match up into something like "Godzilla vs. The Flying Saucer". I'm leaning T260G here, but it's honestly kinda close.
Katrina Lianne Elesius (Wild ARMs XF) vs Chu Chu (Xenogears)
Emeralda Kasim (Xenogears) vs Belial (Wild ARMs 4) - I think creating her own pocket dimension that she can crush at will beats out any advantage that Emeralda's Gear might give her, but it's still a decent match!
Gawn Brawdia (Wild ARMs 4) vs Vayne Aurelius (Mana Khemia: Alchemists of Al-Revis) - This is a pretty close match. Just power-wise, Vayne has the upper hand, since he can theoretically wish anything to happen and that decides the match. However, even at his peak, his control over the ability is really limited. I suspect that Gawn's speed and training may be more than enough to take out Vayne if he's relying on his Mana power of Wishing. However, Vayne's also an Alchemist and has his battle-cat Sulphur that seems to provide pretty solid defense, so he may just avoid/outlast Gawn's assault. Leaning Vayne, though it could go either way.
Altima (Final Fantasy Tactics) vs Zack Fair (Crisis Core: Final Fantasy VII) - Gods tend to be pretty weak in the FF series. They are regularly beaten down by humans, so just by virtue of being a Zodiac Demon, it doesn't mean that Altima wins here. However, Altima DOES possess a young girl, and that's kind of Zack's weakness.
Aya Brea (Parasite Eve) vs Zerase (Suikoden V) - I feel like Zerase has better control over her powers, and even if Aya tries to control Zerase's Mitochondria, there's no guarantee that 1.) Mitochondria from another universe like Suikoden's is compatible, or 2.) Zerase is even human, and therefore may not have Mitochondria. Conceivably, Aya's mutated status may actually make her some kind of demon/undead entity that would be weak about Zerase's Star rune, too.
Warriors
Edward 'Edge' Geraldine (Final Fantasy IV) vs Magdalen Harts (Wild ARMs: Alter Code F) - I just feel like Magdalen kicks more ass.
Nephenee (Fire Emblem Series) vs Delita Hyral (Final Fantasy Tactics) - Perhaps equal in melee skill, Delita is certainly smarter, and has to deal with bigger threats than a spear on a regular basis.
Flay Gunnar (Mana Khemia Series) vs Denam Pavel (Tactics Ogre: Let Us Cling Together)
Oboro (Suikoden V) vs Cliff Fittir (Star Ocean: Till the End of Time) - Oboro may be more clever, but Cliff's not actually unintelligent, and I stand by "Hammer of Might" as taking down most any threat Oboro can come up with.
Karel (Fire Emblem Series) vs Thursday (Disgaea: Hour of Darkness)
Anise Tatlin (Tales of the Abyss) vs Raquel Applegate (Wild ARMs 4) - Raquel wins on intelligence and battle savvy here. Anise has magic, which will be too slow, or her physical abilities with Tokunaga, which is most certainly not the largest enemy Raquel has ever taken down.
Squall Leonhart (Final Fantasy VIII) vs Catiua Pavel (Tactics Ogre: Let Us Cling Together)
Beatrix (Final Fantasy IX) vs Aelia (Valkyrie Profile) - Okay... so taking into account that even though Einherjar are consider minor deities in actual Norse mythology, they are pretty much just undead human warriors in Valkyrie Profile, so that's what they are being considered here. Beatrix, despite being a Paladin-type fighter, doesn't seem to actually have an anti-undead tricks, so no advantage there. Aelia is definitely one of the stronger warriors in the VP crew, and that handy little ability to turn into a Dragon, even for a short while, is good enough to give her this match to me.
Civilians
Ryogo Kusama (Front Mission 3) vs Cid Kramer (Final Fantasy VIII)
Gina (SaGa Frontier) vs Elmo (Front Mission 4)
Ion (Tales of the Abyss) vs Ryotaro Dojima (Persona 4) - While Dojima's a cop and wouldn't go out of his way to attack the Pope... well, he's certainly more likely to apprehend Ion if necessary than Ion is to go on the offensive. Also, Ion's offensive techniques tend to kill him, so it just seems easier for Ion to submit early.
Niccolo (Legend of Mana) vs Anastasia Romanov (Shadow Hearts: Covenant) - Magical Demon camera probably offsets any warrior prowess Niccolo has. Both are pretty scheming individuals, so they'd have no trouble fighting the other. I feel like Ana has more options to win here. Certainly, as an heiress, she could just pay off Niccolo.
Chiepoo (Suikoden IV) vs Edward Chris von Muir (Final Fantasy IV) - Chiepoo is probably the better fighter (debatable), but again, I'm going with the logic of "Edward HAS money, Chiepoo WANTS money, a deal is arranged."
Peasley (Mario & Luigi: Superstar Saga) vs Arnaud G. Vasquez (Wild ARMs 4) - I don't know what Peasley does, but Arnaud flies a jet into him.
Nanako Dojima (Persona 4) vs Teta Hyral (Final Fantasy Tactics) - Teta can't bring herself to harm an adorable little girl who sings the Junes jingle. Nanako for Godlike.
Tengaar (Suikoden Series) vs A Rabite (Mana series) - Hmm.. I'd never thought of Tengaar as a basic human, but I suppose technically her Earth Rune isn't all that special in the Suikoden world. It's still enough to take out a Rabite, though. And as a JRPG PC, we implicitly know that Tengaar has no problems attacking wildlife.
