So apparently in Pokemon X & Y at the "Battle Maison" there is a woman who seems to be trans. She says she used to be a Black Belt, an all male trainer class.
In Japanese, she says
which literally means "To think I was a Black Belt just half a year ago. Modern medicine sure is amazing!"
as an extra bonus, Black Belts are referred to in Japanese as カラテおう, which means "karate king" and is explicitly male.
(extra extra bonus: she is a known thing in the Japanese fandom and there is (somewhat tasteless) fanart of her.)
Good job Pokemons! I am surprised it was handled as well as that even for such a small appearance.
Via the tumblers