Those that doesn`t have to be resized (Snake, Sonic, Mario, Luigi, Peach, Rosalina (?), Link, Zelda, etc) can stay up to their original scale. But there is a lot of those that don`t (Lucario, Pikachu, Bowser, Samus, Ganondorf, Kirby characters, Olimar, etc) because it would make them either too small to be visible (or hit by someone) or too big to fit in certain stages (Giga Bowser can`t go through certain parts of Hyrule Temple). So, they resize them whenever they want. And previous games (64 - in the intro; Melee - when match starts and appearance of Giga Bowser; Brawl - just Subspace Emissary) already showed us that none of the characters are really those that we see in their games - Mario can team up with Ganondorf and Bowser to beat Toon Link, Peach or Luigi if player wants it to happen. All of the characters in this games are trophies/toys, so, their canonical size means nothing here.
EDIT: didn`t noticed that you edited your post. Even then, why can`t Ridley be a big boi then if someone who has same size (Ganondorf...at least in TP...i guess...and Bowser) or even bigger (Bowser) CAN? It makes no sense.