Godlike
Rose (LoD) vs. Gaia (Grandia): I...think? Blech, Grandia plot, but giving the benefit of the doubt to something that threatened the entire world over one really strong 11,000 year old human.
KOS-MOS (XS) vs. Fayt Leingod (SO3): Yeah, pretty one sided.
Ghaleon (Lunar) vs. Bhaalspawn (BGs): Dunno Bhaalspawn enough.
Jenova (FF7) vs. Luca Blight (S2): Jenova threatens the world on a regular basis, even if its only small sections at a time. Luca...like Elfboy said; strongest Runeless Warrior in a world where Runes mean everything can only get you so far. Frankly, his little "keep going despite constantly being knocked down!" felt more like stubborness and adrenaline, than anything else; he was inevitably dead once the trap was sprung.
Heavy
Yulie Ahtredie (WA4) vs. Lyon (FE8): What was Yulie's plot power again? Honestly, can't remember it being that dramatic. The whole Material thing didn't really represent itself outside of gameplay, and her other powers felt useless in battle. Meanwhile, Lyon's still a high class mage using forbidden magic and all that, enough to threaten armies.
Jade Curtiss (TotA) vs. Jet (WA3): Can't vote.
Ashley Winchester (WA2) vs. Basch fon Ronsenberg (FF12): Basch is in heavy...why? He's skilled warrior, yes, but...that's not going to get him that far. Oh, yes, he nukes one bot with a Mist Charge, but FF12 made it clear you can't do that at will, and it was more of a last resort.
MEANWHILE, Ashley has the powers of Lord Blazer AND Argethalm going for him. Knight Blazer or Sword Saint form, doesn't matter which you allow, both are much stronger (combined with the usual ARMs hype being > Regular weapons) than anything Basch has.
Pent (FE7) vs. Georg (Suikos): Unsure. Seems evenly matched from where I'm sitting. Kneejerk says Georg since Pent's strength seemed more intellectual while Georg was more a badass fighter through and through...yeah, that works as a tiebreaker.
Middle
Lucca (CT) vs. Zalbag (FFT): Lucca isn't much of a fighter, Zalbag...is hyped to be the strongest in Ivalice, equaled only by Orlandu and his father. This isn't particularly close.
Tio (G2) vs. Angelo (DQ8): Robot built for fighting vs. above average warrior.
Humphrey Mintz (Suikos) vs. Eclair (La Pucelle): The Dark Form was genuinely threatening from what I remember, and Eclair's suppose to have gotten STRONGER after the whole resolve with it, so...
Jean (Lunar 2) vs. Shadow (FF6): Shadow's plot powers are pretty undefined. Jean, meanwhile, is a complete badass martial artist who surpasses Lunn, who was no slouch himself.
Light
Liz (WA2) vs. Ramus (Lunar): Liz pretty much has the ability to deny death simply by using bizzare philosophy. Ramus has the power of bribery...which is something Liz doesn't care about.
Tony (WA4) vs. Sue (G1): Tony has a mech that blows stuff up, Sue has a little animal riding her head that can breath some fire, and dance with pom poms.
Ovelia (FFT) vs. Shir Gold (PS2): Shir is a thief and wields knives. Ovelia has absolutely no battle experience whatsoever, meanwhile.
Ozzie (CT) vs. Peppita Rosseti (SO3): Ozzie can make impenetrable walls, and has a laugh; this lets him block out Peppita's annoying rambling and allows him to ignore her performance, and without those, Peppita runs off crying!
(yes, I wasn't being totally serious with my reasons for Light, but my votes were based off serious reasons <_<)
