I return from my slumber. This post consists of a couple ideas I've had but haven't been able to expand into their own posts, so there might be more on these things later if I think of more.
I've mentioned before that the Dreamcast has a full lifespan and is the console for fighting games in its time. And one fighting game on the Dreamcast is Marvel VS Capcom 2. That game does better in this timeline than in real life, well enough that Marvel is willing to maintain a stronger relationship with Capcom than in real life. Capcom still is a bit leery of making new fighting games before Street Fighter IV, but they do port Marvel 2 to more consoles and agree to license out their characters for a Marvel-produced line of comics. This line happens to go into production in the middle of this timeline's Ultimate Marvel getting rolled out, and the decision is made to follow that approach, partly because they can already see that it works and partly because it lets them hedge against Capcom deciding not to renew the license. And so the Marvel comics about Capcom characters tell stories that are designed to come to a definitive end, at least for the initial wave. These first comics do well enough (though in part because of the novelty) that more get greenlit, and these ones do like some previous Marvel licensed comics and actually integrate the licensed characters into the mainline Marvel universe (in particular, I'm thinking of what Marvel did with Conan the Barbarian and ROM the Space Knight here). Among other things, this means that the Marvel VS Capcom games' implications of Spider-Man being friends with Morrigan Aenslad become canonical.
As for what happens in that initial wave of Capcom comics, they're sort of an adaptation of the Marvel VS Capcom games, though mostly in terms of the concept, since the actual games don't really have a story. Two universes, both alike in dignity, get fused into one, and the heroes of both fight each other, team up against villains, have cool moments, part ways as friends, all that good stuff. Once the decision is made to actually integrate Capcom's characters into Earth-616, that initial story gets retconned into something that happened in Earth-616 as opposed to a standalone universe, except that Earth-616 and Earth-Capcom (I'm not sure what number they give Capcom World, maybe one that works as a Japanese number pun) didn't unfuse. And then there's a bunch of stories involving Capcom characters, either on their own or interacting with Marvel characters. What they are, I'm not sure, but there'd definitely be good stories and bad stories alike.
This sort of collaboration gets Marvel management thinking about trying to break into the Japanese market more than they previously have. American comics have had a presence in Japan, but never very much of one, as far as I can tell, and the example of Capcom letting Marvel adapt their characters to fit with how Marvel does comics (there is a requirement for someone from Capcom to approve what Marvel does with their characters, but that someone ends up being an American who likes comics, so Marvel gets a lot of leeway) means that Marvel decides to find a Japanese company to partner with to bring Marvel's characters to Japan in a way that fits what Japanese audiences will go for. Eventually, this results in Marvel working with one of the major manga publishers (I'm not sure which) to produce manga about their characters and later anime adaptations of those manga. This includes characters like Spider-Man (who gets reworked into something like a Kamen Rider) and the X-Men (which does mean that in this timeline Kitty Pryde is technically one of the few Jewish characters in anime), naturally, though there's no doubt other characters that get their own manga/anime. I'm just not sure who would be big enough in a timeline where the MCU isn't making the Avengers into anything other than a dumping ground for C-listers. Maybe the Guardians of the Galaxy, since I remember hearing that Rocket Raccoon was added to Ultimate Marvel VS Capcom 3 because the (Japanese) developers thought he was neat, and I could see that meaning he'd get considered for something. Other than that, I'm not sure which Marvel characters are getting brought over to Japan in this timeline.
The Marvel manga/anime definitely get a significant commitment from Marvel's side since it's a pretty big market they want to break into, but I'm not sure how well these series would actually do in Japan. They'd almost certainly get re-imported back into America, and there I'm sure they'd do fairly well (popular characters and anime is fairly well-established in America by this point), but in Japan I just don't know. Considering the real-life success of My Hero Academia, I don't doubt that American-style superheroes can find an audience in Japan, but it'd depend a lot on the skill of the people actually making these adaptations. Budget wouldn't be an issue, Marvel's committing to this, so if these things fail it's not because they lacked production value. If I figure something out, I'll post about it.