Godlike
Prototype Gear (Wild ARMs 4) vs Caineghis (Fire Emblem: Radiant Dawn): Been Discussed.
Izanami (Persona 4) vs Tir McDohl (Suikoden Series): I remember it being durable and not having fail damage, so...sorry Tier.
Cidolfas Orlandu (Final Fantasy Tactics) vs False Althena (Lunar: Eternal Blue): Avoids OHKO with White Robe, Night Sword vs. low HP should insure full healing.
T260G (SaGa Frontier) vs Ameno-Sagiri (Persona 4): Trash-can no like gravity.
Heavy
Kanon (Wild ARMs 2) vs Lashiec (Phantasy Star IV: End of the Millenium): I'll explain later below, but Kanon doesn't beat durable bosses.
Pamela Ibis (Mana Khemia: Alchemists of Al-Revis) vs White Rose (SaGa Frontier): Yep.
Renee (Mana Khemia: Alchemists of Al-Revis) vs Lenus (Legend of Dragoon): SLug fests.
Oerba dia Vanille (Final Fantasy XIII) vs Delita Hyral (Final Fantasy Tactics): YEp.
Middle
Fina (Skies of Arcadia) vs Sceptile (Pokémon): Should kill before Fina gets anything notable off.
Caina (Wild ARMs 2) vs Ray (Fire Emblem: The Sealed Sword): Looks like Ray squeezes a win.
Albert Serdio (Legend of Dragoon) vs Natalia Luzu Kimlasca-Lanvaldear (Tales of the Abyss): Think she can outlast this.
Zegai (Suikoden V) vs Lufia (Lufia and the Fortress of Doom): lack of speed kills him.
Light
Jogurt (Shining Force) vs Sheena Fujibayashi (Tales of Symphonia): ...it's Jogurt...
Raticate (Pokémon) vs Zieg Feld (Legend of Dragoon): Raticate didn't totally fail at everything the way Zieg does.
Bard (Final Fantasy V) vs Viki (Suikoden Series): EDIT: Forgot Viki4 does have instant death, but not sure I vote on that; she has multiple forms that all work the same way, and one which is cleanly better...feels wrong voting for that one, for me, so yeah, sticking with Bard.
Nanami (Suikoden II) vs Blank (Final Fantasy IX): in the end, Nanami is faster and screw it, I'm going with that because seriously.
...
I don't vote on Boss Kanon for simple reason: She spends notably more of the game as a PC, and is fully memorable as a PC. Furthermore, Boss Magus has a legitimate Plot Reason for being stronger than PC Magus that being he got outright drained by Lavos. Also, and this is kind of significant, PC Kanon is not an optional split path PC, Magus is. Seriously, the two are not as 100% similar as you guys are making them out to be.
Also, where is this "heavily implied she's overclocked her boss parts" thing? Watched the scene after her 3rd fight, it just says she was relying on the Sword Magess blood, thinking it was going to work, and lost. Nothing in the way it's worded do I see can be twisted to mean "maybe they meant this." Also worth noting that unlike Kanon, Magus has a 2nd Boss fight where he actually can only use the 3 Level 2's and his physical, thereby consistent with the power drain. Kanon...might use a few moves in boss form she can't use as a PC initially? Seriously can't remember details there.
Though, even if we assume the "overclocked" argument, doesn't that imply it's an exceptional circumstance that she can get this strong? Because where does the game imply that either she's still not doing this, or perhaps later on she starts doing it again now knowing how to control it better?
It'd be like allowing FF9 characters Trances because of Heightened Emotions plot consistently whenever they fight specific foes.
Also, I highly disagree to "Kanon is more memorable as a boss." She's only memorable as a boss because she doesn't fail in game like all the others, but she's more memorable as a PC due to being game best speed with attacks strong enough to OHKO randoms and does good damage vs. Bosses. I can't even tell you where 2 of her Boss fights are, and I played the game twice (I remember Emulator Zone at least because it's kind of a surreal dungeon like that.) In fact, when she first joins, you don't even have Brad, so she's one of your main damage dealers for a while.
Granted, this is all arguable, but in the end, "more memorable" is a subjective argument, and one that doesn't go very far in either direction.