Since they rarely ever do big changes, and causing him to be too good is something they clearly don't really want, these are some minor-ish tweaks I'd like to see.
Please don't step on me giant lady...or do, what does it matter anyway?
Black Widow - I like her kick and stun. Actual great ability. I'd personally change everything else, including her rifle and the awful sound effects it has. The fact that running is one of her abilities is another thing as well.
Mr. Fantastic - Change distended grip to a completely different ability. That ability is just bad. Change his ult. There's a lot of possibilities but maybe adding something where you can change between doing smaller and faster bounces or larger ones with more damage? That would be cool.
Ironman - The way his missles work in overdrive, make those work the same in his normal state, or change the ability. Making the flying animations and transitions more smooth would be nice. Also, give him 25 hp worth of shield during ult. Why not?
Psylocke - Change the winged shuriken ability (I think that's what it's called? The one where she gets shield from the shuriken). Just a boring ability. She could have something more interesting.
Storm - Change the lightning bolt to something else, make it bounce off targets, or just change the ability.
Hawkeye - I'd change sonic arrow into something else.
Human Torch - Give him his old primary fire with the wider, shotgun type spread. I really hate the current primary fire.
Magneto - I like his secondary fire, and idk how they'd change it, but his primary is just...one of the most sleep inducing things in this game.
Peni Parker - Her primary fire also sucks, adding a secondary fire would definitely help make her playstyle more interesting.