The sad thing is that, were it not for all the hub-bub and the internet making such a huge deal over how "this is a huge win for trans rights" and all that, I'd honestly consider this to be something that I wouldn't have as much a problem over. Her gender is something that the game doesn't focus on or make the main thing that her character is centered around. Heck, it's only tertiary to her main development of growing a backbone and joining the heroes.
If you're going to include these sorts of things, then at least do it in a way that doesn't make it the only thing a character has. Which, come to think about it, is something that a lot of these people tent to do.