Now I know what your thinking, but this idea is very different than most. Just look at my character as i am a guy and I play both genders. This character captures that aspect in true essence, it can be adapted to another series if I have seen it or know enough about it. This scenario has always been interesting, as it allows me to play both at once and yet play neither as well.
Anyways here is the GSD based plot.
It is just into the war and the fleet has taken off after the thieves who stole the mobile suits, however back on the plant what is thought to be a natural spy is caught and their existence is denied by their own people. Reality is this person is a traitor and responsible for the deaths of several soldiers due to his unknown actions there. While everyone assumes that he is a guy and will for a while, he is really a she in disguise on the run to escape justice back home. Thus they get caught up in the war against the naturals as it is evident they know how to pilot and in fact are not fond of their own people, but the truth of their double life when discovered will lead to serious complications and truths about what really happened.
If you want a different anime base let me know, I am in an anime base mood. This can also be as extreme as we settle on, you can be either female or male. But I was thinking that upon discovery the character who finds out uses it as leverage, and my character is forced to honor their requests.
Other animes I know I will send you a list upon request, via PM.