For now, I'm going to talk about my issues with Kanji and Naoto (as individual characters, not as a pairing) in Persona 4.
The thing is, if they had been presented to me differently, I would have really liked them--especially Naoto, because yeah, there are a lot of reasons for a girl to want to present as a boy to the world and to feel inadequate because she has a vagina. If they had been presented to me differently, I probably would even like the pairing, because they're cute.
And they're not bad characters, or even bad concepts for characters. Boy who is angry and insecure because he doesn't fit into the socially defined rules of masculinity? Great! Reserved, serious girl who feels like being a girl interferes with achieving her professional dreams? Golden!
But this is how they were presented in the game, particularly their dungeons:
Kanji: "I have girly interests, so I'm scared that I'm gay! I'm going to have a huge sexual identity crisis over this! Whew, but it turns out I'm not gay after all, just confused!"
Naoto: "All the fictional detectives that inspired me as a child were male, and people would take me more seriously if I were male, so I disguise myself as male and wish I could have a sex change operation to make me male! But it turns out I don't need any of that, I just need to accept myself as I am!"
The narrative of the gay teenager who's just confused is a common one. Good liberal parents who are fine with teh gays getting rights but not with teh gays getting their children throw it at kids who come out to them all the time. I got it ("Look, I think you might have read a lot of things that made homosexuality appealing to you, but..." Thanks, Mom). Yes, there probably are some people who spend years anguishing over how they must secretly be gay because they don't fit rigid gender stereotypes, but really they're straight and only confused...but much more common are actual gay teens who are belittled and devalued by being told that they're just confused.
Seeing this narrative validated in my happy fun video games hurts.
Naoto's story is a little trickier. Transgendered people are even more marginalized than gay people, and therefore transphobia is generally harder for the cisgendered majority to recognize. But skim any transphobic essay, be it from the right or the left, and you'll come across this narrative repeatedly: "You shouldn't alter your body. Your body is fine the way it is. You just need to learn to accept yourself the way you are." Which sounds nice and warm and fuzzy to cisgendered people who know nothing of what it's like to be trans, but it erases the reality of trans experience: that even if you do "accept yourself the way you are," you still feel like your body is wrong, and taking steps (hormones, surgery, whatever) to fix that is what makes you feel better.
It's particularly aggravating in Naoto's case because her story didn't remotely need the looming threat of a terrible, ghastly SEX CHANGE OPERATION. The only reason for having it there is to feed into the transphobic fear that sexual reassignment surgery is mutilation. Come on, this is a Shin Megami Tensei game; they could've come up with a much better way to scare us.
In conclusion, I really want to like Kanji and Naoto. They're super cute. I just wish their stories weren't tainted like this.
A side note: thanks to some cues in the new ED, I have finally pinpointed exactly what Gundam 00 is doing with Lyle and what my problem with it is. I may talk about this later.