Mewtwo is either genderless or hermaphroditic(both male and female at the same time). Voice has NOTHING to do with gender.
Same sex as the Mew it was cloned from, either sex due to undisclosed level of genetic modification by the scientists that "improved" upon Mew's DNA when creating M2, or sexless due to aforementioned genetic modification (and game data).
Strictly speaking (har har har) I don't think Mewtwo has ever spoken; its male voice in the first movie was telepathy, not vocalization. As a matter of fact it could be entirely possible that the "sound" of its telepathic voice is entirely determined by the receiver as a subjective experience; I don't believe any character made mention of nor compared the exact "sound" of its voice and for all we know different characters may have heard different tones or coincidentally interpreted it similarly as a male voice due to Mewtwo's imposing physical stature and implicitly/explicitly menacing power being typically masculine by human standards.
That or I have no real ground to stand on when making this argument since I only saw the first two movies and parts of the third and basically none of the show that would be relevant to this discussion, just my (mew)two cents. --- Don't get hit and hit it until it dies, in that order. Kill it, carve it, wear it, repeat it.