This seems weird to me too. It's incredibly obvious that Mewtwo X is meant to be the masculine one and Mewtwo Y is meant to be the feminine one, so shouldn't the one with a Y chromosome be the male one?
Obviously X is the feminine one, it's covering itself up a lot more (the lines on it definitely look more like it's wearing clothes or an outfit, especially in comparison to Y). Y is all out there, so it's gotta be a man (lulz). Plus, look at the size of that tail. Also, Y's horns are more threatening looking. And it's not like feminine men and masculine women don't exist.
This is mostly a joke if you can't tell, but it really isn't "incredibly obvious" either way.
People are thinking about this from too clean a perspective. Of course there will be human characteristics and or human views on gender characteristics, because this game, invariably, is made by humans.
Warning: reader discretion is advised for the preceding post! Read it, it's funny!