I mean the playing with the idea of him being gay is sort of accurate ? At least when I was in high school being a male with feminine traits tended to get you labelled as gay or terms with similar implications (like sissies). Admittedly that was around the turn of the millenia in a rural Queensland (Australia) town. Gender and sexuality were kind of interlocked at that point in my experience. The wouldn't it have been bad stuff is bad yes.
I'm not sure how to respond to the bit on Naoto. I don't understand what about Naoto would preclude her crushing on protag. Or why that would be more anime hijinks than every other high school aged female S-Link in the game. Like some of the choices in her S-Link are creepy yeah, it ain't my business to tell Naoto how to express her identity (and more so the romantic route).
The game doesn't play with Kanji's sexuality in a way that's remotely natural. Forget the feminine hobbies thing; he goes from having doubts about his sexuality, to 100% crushing on Naoto, with a near perpetual stream of reminders that he's "not like that anymore!" There was never a sincere attempt at portraying him as someone with a fluid sexuality beyond his initial arc, so it's not accurate in the slightest.
With Naoto, it's convenient how she starts becoming sexualized/crushing on you/etc after her gender is revealed. To quote Marmaladefire, it's almost as if they're soothing the players potential fears by reiterating that Naoto was in fact, a girl the entire time. Even Yosuke puts it into words by literally saying "you really are a girl after all!" Naoto's gender identity issues run pretty deep in her arc, but they don't really treat it all that serious after her initial arc concludes. In fact, they don't revisit, ever.
Part of this feels like questioning why you can date pretty much everyone of the opposite sex (and sometimes some of the same) in dating sim games. Which 3/4/5 definitely took cues from. The time management portion is like a straight out transplant from that time period. And those games aren't meaningfully different today than in 2007, except perhaps for them being well known enough to have ironic/parody versions as a sub-genre now.
I'm not questioning it, but using it to further my point. Instead of improving the romance system or making it more varied, they rigidly stuck to the same rote dating sim set up from P3 and P4. It's worse, given how you can romance
every single female character in the game, which is something you certainly could not do in Persona 4. It's a blatant regression.
And as to why some Hugh schoolers make gay jokes well that happened when I was at highschool and judging by anti-bullying programs with focus on LGBTIQ issues that exist in Australia it doesn't seem like its stopped. And Yosuke generally wasn't treated like he was being a dick because he was. The representation of gay people in Persona 5 though, is just fucked up no question there.
The "Yosuke's just a teenager, so of course he's gonna make gay jokes" defense is so played out right now. The issue isn't coming from Yosuke himself (the intent is to portray him as immature), but it's
how the game's frame it that's the problem. His many insinuations that Kanji is gay is ultimately treated as "playful jabs" on his part over outright bullying. Yosuke and Kanji almost have this pseudo comedy routine where every time Yosuke implies he's gay, Kanji threatens to beat him up.
Atlus literally sees this as comedic.
And you bring up what it was like in your highschool, but homosexuality is treated far worse in Japan since it's a society that generally shuns people that are different. Anti-bullying programs are non-existent, and teachers outright avoid you if you confide in them about being gay. And we know from Persona 5 that Atlus doesn't take the concept of homosexuality very seriously, hence my original point. They were never portraying Yosuke's homophobia as a "douchebag, uninformed highschool thing."
So as I said originally, Atlus is ironically indulging in the status quo, the same status quo that Persona 5 spends most of the game criticizing. While modern Japanese games like Nier 2 and Fire Emblem: Echoes have made great strides in representation, Atlus is still stuck in the past. Hell even the people who worked on Persona 1/2 were more progressive than the newer team. Which is absolutely fucked when you think about it.