I get that an original story would make more sense, but I'm most intrigued to see a Galactus/Secret Invasion type story, as well as a part of the story that involves killing/saving Jean Grey (Referring to Mephisto's Realm and saving Nightcrawler). At the end of MUA 1, we saw Galactus crushing a hologram of Earth, and instead of the second or third game being about his revenge, like many probably guessed or assumed, the second one was about the Civil War comic line and the third one was an original story about the fight against Thanos or something. I really think it'd be interesting to see that after all the "fighting on separate sides" and "fighting off a tyrant" bs that we finally get to see Galactus make his move and make an attempt to consume Earth and even see the return of the Silver Surfer. It would also be great is MUA 4 made callbacks to MUA 1, 2, and maybe 3, depending on how you want it. And lastly, the timeline thing, in which small side quests have a big impact on the future is what I'd also like to see, as that was an interesting concept and ties more into the Marvel storyline and gives us more information about certain things. It'd also be cool if The Watcher makes a return and voices over the "Timeline summary" and stuff, that'd be super cool, and so were the simulations. Simulator discs were great, as some of them would be you solo against a villain in one room, and others would be your team of 4 against one villain. All this and more would be amazing to see in a new MUA at some point or another.
That sounds like a great idea!! They can retcon MUA3 to be in the same universe as the last 2 games in the fourth game if they ever make one. Plus, all the things you said would help the franchise bring itself back to greatness. This time, it could be on multiplatform