Godlike:
Lugia (PKMN) vs. Johnny (SH3): What Elfboy said, combined with how Lugia's probably one of the weakest ubers for Plot Power, honestly. He's not a genetically created super freak like Mewtwo, doesn't control forces of nature like the Weather Trio, can't resurrect things like Ho-oh apparently can, doesn't control TIME AND SPACE like Dialga and Palkia, etc. I suppose it makes sense why he's such a pure defensive Pokemon in battle <_<
Dart (LoD) vs. Guv (DQ8): Guv's plot power is essentially "immunity to curses" from what I recall. Dart, meanwhile, has at least 2 Dragoon Stones, and one of them is the Divine Dragon which we know is totally bad ass.
Lucia (Lunar2) vs. Dante (SMTN): I kneejerk Lucia, except Dante has a way of beating the impossible.
Aya Brea (Parasite Eve) vs. Ryu3 (BoF3): Ryu has the entire power of the freaking Brood going for him, combined with apparently being able to stand up to Myria, a goddess (and if someone uses Monkey's rant from before, Myria HAS proven herself quite capable at this; she did, afterall, quite literally manipulate the nature of an entire world.) Aya...is like Guv; her main advantage is just that she can't be hurt by the villain's shenanigans, and her own cells are effectively poison to it. I don't recall her having any sort of super human powers beyond that.
Heavy:
Reis (FFT) vs. Argilla (DDS): Does Reis have any real powers besides taking traits of a dragon (and not being of the BoF series <_<)? Cause I'm thinking "Turn into a demon" would be better than that.
Geno (SMRPG) vs. Flik (Suikos): Flik's a strong warrior and all that...but thinking "Star Protector" or something is somewhat better.
Hugo Hewitt (WA4) vs. Tear Grants (TotA): One controls Time (to a degree), the other is just a skilled mage. I also agree that Hugo should probably be up a rank.
Edgar Roni Figaro (FF6) vs. Cecelia Lyn Adelhyde (WA1): Edgar I feel is a plot middle, cause his mechanical genius in game only really comes off at situational moments (Figaro Castle). Cecilia has Mediums and such, at least.
Middle:
Dryst (Brig) vs. Umaro (FF6): Umaro can bust down walls effortlessly, which should give him a leg up on Dryst <_<
Deneb (OB) vs. Juan (S3): Juan's plot power is um...not much at all; his fighting style is more a parody that I don't take seriously. Deneb, meanwhile, is treated as one of the greatest magicians in that universe, from what I recall, and even created her own brand of magic too boot.
Elena (FF7) vs. Zelos (ToS): Zelos has the whole Chosen thing and even some artificial magic powers. Elena is an inexperienced Turk, which isn't THAT weak, definitely puts her below Reno/Rude.
Seth (FE8) vs. Garet (GS): Gonna kneejerk and say that Fire Adept > Seasoned Vet.
Light:
Tia (Lufia2) vs. Roger Bacon (SHs): Roger Bacon should probably be higher, since he WAS a famous warlock and probably still has magic and such. Tia is completely inexperienced fighter meanwhile.
Leena (CC) vs. Margie Fatima (XG): Leena evidently doesn't mind fighting, given she actually fights. Margie...is at best a cheer leader.
Alfred Schroedinger (WA3) vs. Lulu (S3): One has dynamite and knows how to use it effectively (...in plot.) The other's most famous moment involves himself getting killed while charging with a knife. If nothing else, I picture Alfred throwing dynamite and Lulu charging said dynamite head on, followed by Alfred face palming at the moment <_<
Poco (AtLC) vs. Lute (SaGa Frontier): EDIT: Super explained it best.