Godlike:
Miang (XG) vs. Terra Branford (FF6)
Yeah, even if Terra does win, she loses. Especially if Miang randomly gets Terra as her next "volunteer".
Lloyd (LoD) vs. Althena/Luna (Lunar1)
Althena > Dragon/Melbu Frahma
Heavy:
Zack Fair (CCFF7) vs. Cliff Fittir (SO3)
Cliff is considered better than humans, though his big advantage is immunity to certain things. Zack is better than augmented humans (though not the best, he's near the top) and it takes a small army of modern troops to bring him down.
Alis Landale (PS1) vs. Selan (Lufia2)
I'm going to be different here. Sure, Alis is just a runaway, she's also the original Algol Protector and first inheritor of Elcydeon, the sacred blade of Algol. That gives her destined hero status, which is better than trained soldier plot-wise. She also lives, whereas Selan wasn't going to live, period.
Middle:
Bart Fatima (XG) vs. Flik (Suikos)
Suikoden 1 Flik would lose this. But the job he does growing up before Suikoden 2 changes things around. As it is, not only does he face off a castle full of angry grunts with only one buddy and lives, he's the competant save your ass guy in the second. Bart? He's the semi-competant get your ass in trouble guy.
Mia (GS) vs. Relm Arrowny (FF6)
Mage-Knights and Psyenergy adepts are both big deals. It's just that one is kinda funky and not really worth much anymore, while the other is a strong and useful tradition, when it exists. And that gives Mia the win.
Miranda (G3) vs. Nanami (S2)
She got the same training from a small-time hero that the two mains got, and has the same kind of headstrong confidence that Miranda has. Not to mention, she doesn't sleep with Alonso or try to hook anyone up with Alfina.
Light:
Jessica D'Alkirk (Lunar1) vs. Hix (Suikos)
Why all the Hix hate? He's the designated next leader of a village of warriors, has some respect from their leader, and the love of his daughter. That's not nothing. Especially since even while he is pushed around and tries not to fight, he will do so willingly and eagerly when the stakes are right. Of course, he's up against a combat loving, divinely powered, beast woman with a spiked club. So, uhhh.... yeah.
Razzly (CC) vs. Deneb (OB)
Considering your choices on Deneb influence your popularity, this means that people care about her. Razzly... I guess the fairies aren't as happy if you don't rescue her? But a province > insignificant fairy community for importance. And this is before considering Deneb as a force for magical innovation.
Taloon Torneko (DW4) vs. Jelanda (VP1)
Sure, Taloon is craftier than Jelanda. But you have to consider, she's a god, so people can't hurt her all that much anymore, and her favourite response when things go wrong is to make the offending thing go boom. Something she is fully capable of making happen. Besides, hanging out with Lenneth means that your character flaws get bought off.
Cid (FF6) vs. Puffy (Grandia)
Sure, Puffy can breath fire, but Cid can make mecha that can breath fire, ice, and lightning.