Funny story, actually.

There is this Japanese equivalent to the ESRB in Japan called CERO and, not too differently from ESRB, they have some questionable definitions regarding what constitutes mature content. As it turns out, for some odd reason, anything resembling short skirts exposing bare legs is instantly grounds for a 15+ age rating from them, and Smash wants to stay E 10+, so they opted to not have any characters show exposed skirt legs, thus making Pyra's outfit passable despite being just as explicit, simply for not being a skirt.

Welcome to Japan's odd mature content standards.

You know, why did Pyra's outfit not get censored? I mean, considering the initial hoopls over the game's character designs started with her, you'd think someone at Nintendo would decide to cover her up…