This is actually sad because before Persona 5 became mainstream it was moderately chill for JRPG standards.
Persona 4 is when SMT as a whole took off, and it really wasn't the vanilla PS2 version as much as it was Golden, as all the insane progressive shit didn't really exist in force back in 2008. From there we got two Persona 4 fighting games (with plenty of P3 content) and the first rhythm game was also Persona 4. Like with most things in current year thanks to the power of The Internet, it's really hard to say who was into what, and how popular something was, but before P4 surged, it was a sleeper hit, as most Atlus games were.
Persona 1, Persona 2: Eternal Punishment and Persona 2: Innocent Sin were drastically different from Persona 3, which became the standard for what the games would become. I'm not gonna get into the weeds about what version of Persona 3 was best, because it's a retarded argument of the modern audience screaming the female protagonist is better or better quality of life changes from the vanilla Persona 3. Persona 3 was also more depressing than 4 or 5, as the main character's fate is death; Makoto doesn't get a happy ending with his friends, he's destined to die to prevent Nyx from wiping out the world. The Persona games are also easier than the other SMT games, mainline and off-shoots (but only retards like me enjoy Digital Devil Saga).
Now all that aside, for anyone who really wants to get into it.
Persona 4 was where the surge happened, and it's spurned on by the Media Literacy crowd having a very distorted take on two of the characters in the game.
The first but lesser character is the party member Kanji Tatsumi. While the entire playable cast are all high-schoolers, Kanji is the youngest of the group, even younger than the non-combative navigator character Rise. There's a whole event where they get scooter licenses, but Kanji can't because he isn't old enough. But what he lacks in the small age gap, he's by far the beefiest of the group. He stands taller than the other characters, and is a punk, and without getting too into the weeds, the signs are more cultural than what we may understand in the west. But he bleaches his hair, the way he wears his clothes, and other aspects. To top it off, he's introduced more as a legend, as he got into a fight with a group of dudes and fought them all off. So I hope you understand I'm trying to draw the picture that this character is beefy manly type. The twist, is that he doesn't really have manly hobbies. He's good at sewing, because he helps out with his family business. But sewing isn't manly, getting into fights, being a punk and raising hell, that's what manly men do, right. And this is where the media literacy crowd fall on their face, because while I'm not gonna say I'm good enough to elucidate on it, but there are cultural differences between the West and Japan and how we see things. So when it comes time to go to his dungeon, they see him on the midnight channel, he's wearing nothing but a towel and in a bath house, and behaving in a fruity way. Where the modern audience fails is this isn't his inner self saying he's gay (in whatever form they want to argue); it's that he's a confused little boy who unsure about himself and his place in life. I'm not gonna pretend that people aren't confused as kids, especially in high-school when puberty and social pressures and other things hit; but instead of realizing that he's just uncomfortable with himself and his place, and he maybe needs time to work it out, he immediately gets slapped with the Gay label.
I don't have an idea about the Japanese that's used in the game or specifically at his part of the story, but I'd be willing to bet that there was a certain amount of fuckery, on top of changing the way he speaks. During the epilogue of the game, Kanji has worked through his issues, he stopped bleaching his hair and is dressing more in line with social norms. He's figured out his place as a man.
Next is the bigger problem, and by problem I mean having a PhD in Media Literacy is Naoto Shirogane. Naoto's not as hard to explain, but is the one the people of gender cling to more. The story is simple, Naoto is a girl, she's a part of Shirogane family, a family that is a long line of ace detectives who crack the toughest crimes. The issue is, as stated previously, is she's a girl; and gender roles being what they are, especially in Japan, women are looked down on as lesser. This puts Naoto in a spot with internal turmoil, because despite having the lineage of ace detectives, she is a woman, and her family name doesn't carry her like it would if she thought she was a man. So during her dungeon, the scene before the boss is Naoto wanting to become a man, because in the modern world, she wouldn't be second guessed or questioned if she wasn't born as a woman. The media literacy experts fall on their face, because while yes, this is a story of transitioning for what it's worth. Naoto isn't transitioning because it's what she needs to be her true and authentic self that her birth got wrong, as much as it is she feels she wouldn't be at a social or professional disadvantage. The one thing I should press on as well, is that while Kanji was more of a punk and dressed the part, to try and conceal her femininity, Naoto wore a hat and heavy jacket to hide her features; for the school uniform she wears the boy's jacket instead of the girl's blouse. But again, in the epilogue, she's wearing a girl's blouse and no hat, not trying to hide her feminine features; she's figured herself out, without any rainbow flag or pronouns.
I'm sure I'm gonna get replies correcting or adding context, but I'd figure I'd start off with some lore.
Thank you for coming to my TED Talk.
QED