>>54195792Mewtwo is literally female from her appearance in the Genesect movie onwards. Also, considering she's a clone of Mew, and Mew was female (literally gave birth to her. No, that's not a mistranslation or metaphor - they use the literal wording for live conception in the original Japanese), it makes sense that the clone would be the same sex as the genetic donor. Mewtwo may have been a dude in its initial introduction for the whole Rule of Cool appeal for young boys, but the original intent is pretty clear that she was always supposed to be female.
Back on topic, even with the Gen1 stat spread, she's still outclassed by power creep regardless, plus the introduction of the Dark-type nerfs her significantly, since she wasn't designed with that weakness in mind. It's a sad - but inevitable - consequence of being the first 'superpowered' Legendary, as everything that comes after ends up having to be stronger than her.