To be honest (man, that is probably the 28th time i have started a sentence with those words), There aren't many differences between Male and Female two, so i don't think that Sakurai would waste Mewtwo's costumes on her, besides, essentially, it would just be two of each costume, thus impairing Mewtwo's aesthetic options like what happened to Olimar/Alph. You also have to remember that Femaletwo isn't canon, nor is the pokemon anime, and so far, no inspiration has been taken from it. I think that the whole Femtwo has arose much controversy that isn't relavent at all, i mean, OK, a certain species of anything whether clone or not is going to have the same gender, so anime wise one Mewtwo is male, and the genetics for the other deemed it to be Female, Mewtwo never "changed" genders, nor is Femaletwo anymore than a flawed experiment, if anything, the attraction of that movie was moreso for Genesect than for Fakertwo.
But pure canon wise, Mewtwo isn't stated to have a currently known gender, however from physical traits and its cry height, masculine feline/human feature etc. If a pokeball were aimed at one's starter they would probably assume it to be male. nonetheless Melee Mewtwo had a male voice, and despite Mewtwo commonly saying "Watashi" which in Japanese is a more feminine word (though some men use it to refer to themselves in high regard), in Ai No Uta (Pikmin) the Pikmin refer to Olimar (who is male) as Watashi as well, thus meaning absolutely nothing regarding Mewtwo's gender. And calling Mewtwo a new fighter also has nothing to do with anything because during the first Smash Direct, once it was over, on the smashbros site they had the "WARNING! Challenger approaching" thing for ZSS and Yoshi despite them being in previous iterations, so in the 50-Fact Extravaganza they probably were simply saying that Mewtwo is a new fighter... to be joining the roster of Super Smash Bros For Wii U and 3DS.
