Gotta agree about Kanji definitely (I'm almost done my first playthrough and just didn't have a ton of time to spend on Naoto's social link so while I agree with your take I'll reserve my judgement of it a little bit). I mean, at first, especially with his shadow you kind of think he might be gay and having trouble accepting it, but it does become pretty clear that it's less he's gay and doesn't want to accept it as he has things he likes and personality traits that make him think he might be but he doesn't want to be seen as less of a man. Though I do his own confusion and questioning of it is kind of justified considering the only girl he showed any interest in at all was a girl pretending to be a guy.

So sure, in the end he's not gay and she's not transgender, but it does deal with some aspects of gender identity that don't get touched on as often as homosexuality in most media, and I'd almost say it does it better than most other media as well.

Hell, I even think it works really well that you're kind of confused and trying to figure them out the whole way along their journey to figure themselves out. You kind of live it with them in a way that most games, movies, TV, etc. don't manage to get me to do very often.