You're not being entirely fair to both the context and narrative of Naoto though. First off, we have the obligatory Western values applied on to a Japanese frame of mind. That doesn't make how it handles gender and sexuality all that much better, but you do have to keep in mind the particular stereotype that Naoto is specifically attacking is the male domination of certain careers. Naoto in no way was ever supposed to be a trans character in the game. She dresses up as male to avoid the stigma of a female in the detective world, which is the crux of her entire story line. It's not Naoto entirely wants to transition to male, she's more interested in the perks and struggling to come to terms with the fact she is female in a world that favors male individuals. She is struggling for identity, yes, but her character never gets framed as actively wanting to transition. Coming to grips with her femininity is her ultimate end goal as a character and that relationship. It always was. The trans label is something certain communities applied to her after the fact. She's discovering her identity, and that ends up as a woman. A role she is very comfortable with by the end of the game. That's the way the story is told and her character is developed.
Now, I'm not going to sit here and argue that Persona is a paragon of LGBT representation. It most certainly is not and the more LGBT related storylines are not particularly well written or handled well for the Western context of identity. But that's just it, we're applying a western lens to a Japanese made video game where the context and meaning vastly differ from our understanding. Japan has some big problems with those regards to, but Naoto (And Kanji as well for that matter) just weren't ever meant to be adopted by the LGBT community as they were. Again, I think that speaks to a quality of writing that those ideas were left on the table like that, but their character arcs were always about coming to grips with their identities in a world that didn't allow for that. Kanji has feminine qualities and doesn't know how to reconcile those, so he acts hyper masculine. Naoto uses masculinity because she feels insecure with her femininity.
As someone in the LGBT community, I took a moment at these as well. But then I realized why this was happening and just how much of my own ideology I had been projecting on to those characters. Again, their not masterfully or tactfully written, but they're also nowhere near as toxic as your displaying them with regards to at least Naoto and Kanji from Persona 4. The other games may have bigger issues with specific characters, so I can't really speak to those.
Anyway, as for Geno. Seems like the past couple days have been rough on the fan base. I think when you factor in that we might not have any new information about DLC characters until well after February and I think it makes sense to take a bit of a break from speculation. We know the first two post-release characters already and the game just came out, so new information is going to be hard to come by for the immediate future. Joker doesn't specifically really do much to inspire confidence in his chances either.
I also think, for those throwing in the towel, this has been a cycle that should have been it. To have supported a character through thick and thin for a decade, and then have all the factors begin lining up in his favor in a way previously thought impossible (Geno recognized, fan requests getting in, Square on board) and then him missing the boat on the base roster just stings. I've mentioned it before, but it feels kind of like now or never for Geno given everything going in favor of him and the situation... But each time an announcement is made the faith wavers more and more. People pushed so hard for the base game and believed in him so much, and the same for DLC 1. Neither of those coming true hurts a lot.
I don't blame anyone for bowing out now. But I will say, despite a more grim outlook we've got four more chances (or however many until we get a Square rep) to see Geno show up DLC wise. That might be actually forever from now, but it's not over quite yet. A second season of DLC would also significantly give us a better shot, so we as Smash communities generally need to push for that as well.