Mascots with some Respect:
Fubar (Suikoden3) vs. Cait Sith (FF7): FF7 PCs can only be so bad; Suiko Monsters that aren't Shiro, meanwhile, fail to impress.
Koromaru (Persona3) vs. Valefor (FFX): Can't vote.
Blanca (SH2) vs. Volug (FE10): Blanca is replacable, Volug is not, even before factoring how good he is overall.
Pikachu (PKMN) vs. Mog (FF6): Pikachu's claim to fame was basically the only reasonable Electric type...which is no long a big niche now that Magnemite doesn't suck, stuff like Electrike exists in other games, etc. Flipside, Mog freaking rules the WoB, and remains solid in the WoR.
Mascots that still technically count as PCs:
Nils (FE7) vs. Roger S Huxley (SO3): FE Bard/Dancer >>>> Roger.
Prinny (Disgaeas) vs. Foomy (Lufia2): Hey, Prinnies are better than nothing when you first get them! Meanwhile, Foomy didn't even register as existing when he existed.
Healie (DQ4) vs. Boco (FFT): One saves your ass against Ragnar, the other just kind of exists.
Magikarp (PKMN) vs. Guido (Grandia): Becomes Gyarados eventually, which beats Guido! Also, Magikarp > Guido on principle.
Mascots that don't even count as PCs (and Jogurt):
Hanpan (WA1) vs. Nall (Lunar1): Resurrecting you after each fight > Tools! Hanpan has one good scene...but Nall is from Lunar, which sort of offsets that...immensely.
Interceptor (FF6) vs. Mieu (TotA): I found Mieu the forced kind of cute; you know "Little high pitched talking mammal!" thing? Rather than genuine cute. Also pure puzzles. Interceptor is an attack dog and pretty awesome because of it!
Muncie (DQ8) vs. Mognet Moogles (FF9): Munchie did stuff <.<? Mognet Moogles get you a protect Ring eventually, and have various fun stuff throughout the game!
Jogurt (SF1) vs. Navi (Zelda:OoT): Oh sure, Tai, give us a match where Jogurt wins undeniably. Fine, want a reason? Navi made me want to turn Zelda: OoT off repeatedly; if that's not the opposite of contributing to a game, I don't know what is!