Godlike
Belial (WA4) vs. Empyrea (DQ8): Remember, Empyrea was pretty much weakened by holding off Rhapthorne in another dimension and essentially split from the realm where she had immense power. Belial, as I stated before, her power isn't to the magnitude that people are seriously hyping it.
Patriarch Sergius XVII (XS2) vs. Chaos (FFI): Evil Generic 8 Bit Final Boss God of DARKNESS thing vs. Space Pope.
Cidolfas Orlandu (FFT) vs. Zog (BoF1): BoF Dragons have insane plot power as a rule, at least, those that still have power, and Zog is one of those.
Altima (FFT) vs. Myria (BoFs): And Myria tends to match the strongest of them.
Heavy
Darkham (AtL4) vs. Kanon (WA2): Bionic Woman Assassin vs. your generic general.
Brad Evans (WA2) vs. Serge (CC): I think somewhere in all CC's insanity, the Chrono Cross and Masamune are suppose to be some sort of psycho powerful artifacts and Serge has BOTH, that should matter more than a Rail Gun.
Alena (DW4) vs. Zeno (BoF5): Again, she's a generic Warrior Princess, against someone who is a fairly high rank in a society where Power is indicative of everything.
Nina Wyndia (BoF4) vs. Rose (LoD): Nina 4's powers are really not much on plot power at all, Rose meanwhile has the whole Dragoon thing going for her at least.
Middle
Luna (Lunar1) vs. Gafgarion (FFT): Luna's still Althena in the grand scheme of things, and Gafgarion's still a normal, if well skilled, human.
Rath (FE7) 4-6 vs. Mog (FF6): FF6 Moogles > Average Humans and Anthropomorphic wolves according to FF6's few plot scenes! Also, Mog still has minor terrain manipulation <.<
Warlock (S4) vs. Jude Maverick (WA4): WA4 likes to hype its ARMs, matters more than Warlock who has little plot to work off of.
Mid-Boss (Dis) vs. Belselk (WA): Good Fight, actually, though in the end, Mid-boss was defeated several times with no Handicap, while Belselk took down RJ&C once (twice in ACF) and they ONLY beat him due to a handicap being instituted on him in their 3rd encounter, which combined with the whole "Strongest of the Quarter Knights in terms of Battle" thing...yeah...
Light
Galleon (S5) vs. Sid (S2): One of the Queen's Knights implies he's one of the elite and such, compared to Sid whose just another random Star.
Hrist (VP1) vs. Seth (FE8): Normal Human vs. Hrist, who while weakened, still is somewhat stronger than your average human.
Gadget Z (S3) vs. Jin Uzuki (XS2): Being able to turn INTO a Giant Mech > Boarding one works as a tiebreaker >.>
Rufus Shinra (FF7) vs. Virginia Maxwell (WA3): Rufus is a normal human with a shotgun. Virginia is one of 4 people who can access Mediums, and wields ancient weapons with actual practice and talent in using them (where as Rufus just kind of grabbed a shot gun and starts firing as far as we know)...yeah...