yeah I linked an article earlier that talks about it, just one of dozens that document everything that has been seen in their games and how the company seems to value that hateful agenda as well as some of their fans supporting it too/harassing people who speak up against Atlus' stuff.
I have nothing against anyone who liked that games and enjoys them for what they have to offer like the gameplay or send of the characters yadda yadda yadda that's all fine, it's just personally bi don't want to support them and I don't think that their current message they are pushing should be accepted by people, and I'd hope that fans would call them out on it so that maybe they could change for the better or something.
But yeah, still holding out for Isaac as a possible surprise, I also wanted waluigi to join him but considering it seems new franchises being represented only for DLC, unless there's a waluigi game in the works that's considered seperate from Mario, the Dream is pretty much dead for waluigi. But I hope his Camelot brother gets a chance at least
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.