Honestly I think people would be surprised at the kind of stuff that flies here in Japan. It's not at all uncommon to see Japanese actors in blackface on TV, and the "Okama" homosexual trope is still played for laughs all the damn time. It's pretty gross.
With that said, having not read the stuff you linked, I never got the feeling that Atlus/Persona specifically was pushing some kind of anti-LGBT agenda? I heard about the ending of Catherine and that was definitely pretty bad, but I think it lines up with the general homophobia/transphobia that's pretty common in Japan. I'm not saying that to give them a pass, just to say that it's (sadly) not something exclusive to Persona, and you also have to weigh the fact that Kanji, one of the main characters from Persona 4, is canonically gay and (to my mind) was treated fairly respectfully and with actual nuance, by Japanese standards anyway.
That is to say, you're not wrong by any means, and I'm not trying to whataboutism this, but Cloud in Final Fantasy VII also cross-dressed as a woman in a brothel, nearly got sexually assaulted, and Barret is a pretty yikes black stereotype, but it was still cool to see Cloud join the fray in Smash. I think it's OK for people to be excited about Joker being in and it's also OK to feel as you do as well. I just wanted to add in my two cents there and say that I don't think it's quite as black and white as "Atlus hates LGBT." To my knowledge at least they're not on Chic-Fil-A's level at least where they're actively donating to hate groups.
EDIT: as for some of the fans of Atlus' games being pretty toxic, no argument there. But I'm not sure how that reflects on the company themselves. Rick and Morty fans, Kingdom Hearts fans, Call of Duty fans, etc. etc. all have VERY vocal and obnoxious and awful segments of their fanbases but I don't think it's fair to pin that on the company unless it's something that they actively stoke.
EDIT 2: Just because I didn't make it clear in my original post: what I'm getting at is that Japan is a different culture with a different history and different values and we can't judge them by 2018 Western liberal values. That goes without saying, of course. But the progressive movement in the United States and the widespread acceptance of LGBTQ+ individuals in North America and Europe is a VERY recent and far from complete phenomenon, and it just takes time. Japan is still a pretty homogeneous place (not as much as people think but that's another story) with a lot of very conservative worldviews when it comes to stuff like this. I do my best to engage my Japanese friends in conversation about this stuff or call out things that offend me when I see them, but it's slow going.
Since this is a fairly long post and I don't want to go off topic I'll just make bullet points:
>Yeah, I've seen that, I remember the blackface new years thing and it was foul.
> Catherine is the most notable example, but there is many examples throughout almost all Atlus games that basically go even worse, one from persona specifically being the persona 4 game's character Naoto who is specifically coded as a transgender man, and is a perfect example of how they actively discriminate against LGBTQ+ people in their games (specifically trans people in this case). I recommend reading that article to get the full picture as it list the instances of that in multiple games.
>As I mentioned, one somewhat decently done representation in a game is kinda overshadowed when the other ones are so blatently not and are very discriminatory (as I mentioned with Naoto, who is also from persona 4). It's the equivalent of giving a dog a treat while still yanking on its collar and hurting it on it's walk, any good intent or small praise is ruined by the abuse given at the same time.
>Cloud crossdressing isn't really problematic, crossdressers and trans people aren't the same thing, and people crossdress for many reasons, trans people can also crossdress too it's not something exclusive to CIS people. I won't deny Barret thing though for being a blatent stereotype. Personally I like poison from street fighter/final fight who is a stereotype of trans woman, but I still find enjoyment for her character and everything. It's once again not wrong to like certain things (I made it clear in my earlier post), but it is however wrong to push a hateful message in those thing. Poison or Barret can be stereotypes but if people from this groups like those characters still that's fine, it's only problematic when they are being use to push a hateful agenda or something.
>I did say "apparently" for the news regarding in house discrimation at Atlus against LGBTQ+ people as people are still looking into it. And once again even if it's the culture for this to be common place ( which still doesn't justify it since bigotry is something that's part of every culture and is wrong in every culture) if Atlus constantly does that **** on their games it's safe to say they are promoting it out of their own ideals and values, otherwise there wouldn't be an example in almost all their games.
> The problem with that is where the Rick and Morty fans making problems about scezhuan sauce or whatever came from their own thing (it's not like Rick raided McDonald's or cause riots to get it), the thing with how some Atlus fans acted was cause of what was being pushed in the actual games itself. I remember clearly when Cathrine came and the knowledge that a character in it was a trans woman, some "fans" went raiding the wikis calling her a "mentally ill man" and hateful shot like that, and that steams nor just from their own hatefulness, but also from the game treating the character the same way. And since stuff like that keeps happening in their games, yeah, they kinda are stoking the flames :/
>History and everything is irrelevant to that. We live in a day and age where people around the world can interact with almost no Barriers thanks to the internet and everything. It's not "2018 liberal values" it's basic respect morality and understandment should be universal to everyone no matter what circumstances or anything. And like it was said, all cultures have bigotry in one way or another in their roots and history. Doesn't justify seeping into a modern day era. I know tons f people in japan who are part of marginalized groups who have been around for a long time and have experienced discrimination and ****, just the same as my friends in America going through the same ****. Regardless of culture or history or time, hate is hate, and should not be promoted. That's just common sense. And from what I've seen, Atlus has been really stubborn and holding onto that hate. Once again, people can still. Enjoy the character and the games etc, just remember to recognize when the company behind it is doing something that is obviously wrong and be called our for it so they can change for the better.
That's all I'll say about that now since I don't want to get off topic again, but if you (or anyone else) still want to talk I'm free to dm.
Otherwise this is done