Here's my character wishlist:
Playable:
Rocket Raccoon (keep-away character using ranged attacks)
Groot (defensive wall)
Squirrel Girl (Kinda like Deadpool, but more of an ambush character)
Star-Lord (Gets stronger as he's hurt)
Mystique (admit it, copying enemies is really damn cool. Plus, it makes more sense than a playable Red Skull (he's got an entry on All The Tropes's Complete Monster page for a reason), because she's helped the X-Men from time to time)
Baymax (offensive wall. Perhaps he can change between modes (unarmored Disney, armored Disney, original) for different situations?)
1939 Human Torch (because he's Marvel's first ever hero)
Gamora (to even out the GOTG characters)
Reptil (shapeshifting into dinosaurs, WOOT! Plus, he's Hispanic.)
Iron Patriot
Shadowcat
Marrow
Dazzler
Quake
Bosses:
U-Foes (as a group boss, perhaps)
Awesome Android (could later become an assist)
Lady Deathstrike
Ultron
Ronan the Accuser
Apocalypse
The Melter
Basilisk
Terror Device
Bile
Patriot Missile
Godhead
Living Laser
Iron Monger
Crimson Dynamo
Silver Samurai
Abomination
Helpers:
Omega Sentinel
Yondu
Slapstick
Sleepwalker
Scarlet Spider
Toxin
Jessica Jones
Peggy Carter
Awesome Android
Howard the Duck
Drax the Destroyer
Marvel Logo/Xavier helpers:
Red Ronin
Galactus
(Giant-Sized) Man-Thing
New Remake Modes:
The Incredible Hulk (Genesis): Playable characters include Hulk, She-Hulk, Red Hulk, Iron Man, and maybe Groot.