Based on end-game...
Godlike:
Kratos Aurion (ToS) vs. Althena/Luna (Lunar1) - One has a ton of experience under the belt. The other is the evil and twisted reincarnation of Althena - who may have been brainwashed to become so evil, but just by singing she controls one of the mighty dragons and lifts a citadel up into the sky. She also kills Alex if you don't play his flute, and as the legendary Dragon Master, second only to Althena I take him as being somewhat equal to Kratos. Kratos, unfortunately, has no flute. And he has nothing to protect against the fury of Althena.
Alternatively she just summons her Dragons and they deal with Kratos. Works for me.
Kyogre (PKMN) vs. Fei Fong Wong (XG) - Let's say Fei mounts his XenoGears. Awesome shit, man, but then the water level starts rising and Kyogre's in his element. Supposedly hard to beat in the water and rather agile, so long as it keeps away from Fei's destructive powers the Gear will just remain aquatic. And Fei needs food.
Heavy:
Zack Fair (CCFF7) vs. Vahn (LoL) - SOLDIER VS army of SOLDIERS and nearly wins VS lol i has monster on my hand
Rei (BoF3) vs. Lucia (Lunar2) - At her end-game stats, she uses the POWER OF LOVE to overcome the personification of hatred and returns to the Blue Star to watch over it. It is heavily implied with brutal bluntness, to me, that she is back to her old power and perhaps stronger. In other words, Rei's got quite a dandy problem, because Lucia is going to wreck him. And tear him to shreds. And remember, even at the weakest of her powers she was able to ditch Hiro and travel through a canyon filled with monsters (although the monsters may not be exactly PLOT) towards Leo's ship, where she disabled all his petty soldiers but couldn't stand up to his HOLY KNIGHT stuff. Even at the weakest of her powers she's at least as powerful as, say, Garr, so taking her at end-game would see a massive increase in her powers.
Lucia = weak argument not found.
Middle:
Flik (Suikos) vs. Mia (GS) - Badass all around Gregminster in the final scenes, started up his own mercenary group and is known as Flik of the Blue Lightning, one badass mofo. Mia is only known in a single village for curing colds. Well...
Gordon (Dis1) vs. Anise Tatlin (TotA) - Kneejerking that Gordon is sort of competent at what he does and Anise is an idiot.
Light:
Deneb (OB) vs. Jelanda Artolia (VP1) - Jelanda has plot powers beyond Einherjar hype?
Genis Sage (ToS) vs. Blank (FF9) - Can still move while attacking, unlike Genis. Is also competent at what he does. Could probably dodge Genis's first attack and then stab the elf boy. Genis is also pretty easily tricked (Mithos), and I'm quite sure Blank can pull off the same shit. Plus, Blank VS Deneb.