I'm not interested in strict adherence to canonity; my problem is with proportion. Bowser's size constantly shifts from Mario game to Mario game, yes. However, one thing has always remained constant: he is significantly larger than Mario. And in Smash, he is represented as such.
Olimar is supposed to be tiny, sure. But his Pikmin are all proportionally smaller than him, because, well, they are in his own games.
Ridley? Ridley is supposed to be enormous. There's only one game, the original Metroid, where he's not so big, but that game was remade into Zero Mission, where he was scaled up significantly. It's part of his character, and one that should never have been infringed, in my opinion.