Yes please I was going to use the word with three letters when giving the title, but decided to be less provocative.
Anyway, since Crystal, you have been able to choose your trainer character's gender in Pokemon games. What choices have you tried?
I'm not sure if I remember correctly, but I think I did opt for a girl in Crystal but ever since that time I took my own gender. Perhaps.
Then the second part of this thread, where we can use our wildest imagination. Rumor has it that the becoming X/Y games will have more route choosing, so would you like your character's gender affect the plot more or are you happy with a stricter storyline as in previous games? If your answer to that question was that you'd like a more diverse plot, how exactly could the gender affect?
Here comes my solution. If I worked for Game Freak, I'd try some love story: make the trainers your character encounters develop some different feelings. Maybe you could also answer to questions in a different way, like if you had captured the legendary Yveltal, a beautiful girl might ask if you could take her to somewhere flying the Pokemon and you could pick yes or no. You could even make your trainer more attractive akin to the cross-dressing scene in Wall Market, Final Fantasy VII.