It would be cool to play as Iron man then switch to Captain America then Thor (whos in Asgard), and they all have their own places then you are free to roam the city/Earth/universe/realm. Then you have the option choosing in how many characters do you want to use at the same time in free roaming, like you're controlling Hulk and you have Ant-Man along with you and you easily switch them. Then in certain missions you can't choose a playable character, and it can't always be four playable characters in a mission.
Mua lacked flashback missions, so that would be cool as side missions (origin flashback missions). What I'm suggesting would be a lot of work, but it would really separate itself from being another Mua clone. I also believe in quality over quantity, and they don't need to dump every character in the game. Like for this, it would just be the ones that got a solo movie movie + Black Widow/Hawkeye as playables, so thats like a dozen and every single one of them has a role in the story, like it wouldn't be the same withiout them. I'll save the X-men for their own game so as the other teams.