Man, where does this stuff even come from? Your gender is binary, unless you got screwed by genetics. You have male genitals, or female genitals. If you're a female who identifies as a male, cool, that's fine. Then play as a male, or pick female to more closely resemble your current body-type. Whatever works for you. If mentally you feel like you're somewhere in between, you still lean towards one or the other. Pick whatever you're most comfortable with.
This isn't a hard situation to manage. This isn't some stunning revelation to the world. Games that deal with sexuality will have to manage them in an adult way, as it's an adult subject. So yes, you'll want to make sure to let straights be straight, gays be gay, or anywhere on the spectrum that someone may lie. But Pokemon is built for children as its target audience. Children don't even fucking know their favorite color, please, lets not burden them with being gender fluid. The majority of people are raised as their gender, and it statistically isn't really an issue. Yes, there are people that don't fit that mold. But they're *such* an anomaly that at some point a line needs to be drawn. People with physical disabilities are, unfortunately, unable to play some games. That sucks. You don't suddenly become incapable of playing Pokemon because you can't pick "I'm gender fluid."
If this comes off as rude, I sincerely don't mean for it to. I just think that it's important to accept gender fluid people, but also accept that people will always get left out for one reason or another. Eventually, it will happen to you for a reason that you think sucks. Whether it's you being colorblind, or deaf (half-deaf here!), or even just game aesthetics!
Maybe I'm just ignorant to these problems because I'm white and straight.