For any Animated Marvel movies, Marvel should look closely at their characters and make animated movies of those who would never ever have their own movie or wouldn't work in a live action movie.
Animation is meant to be used to do things in animation that can't be done in real life, mostly. So they should use characters they can't use otherwise, and to do stories they couldn't do otherwise.
That being said, some of my choices might work just as well in live action,
but here they are anyway:
the Inhumans
Captain Marvel
Deathlock
Machine Man
Were Wolf by Night
Something with Fing Fang Foom perhaps
Secret Wars (would make an awesome and epic movie)
3d-man
the agents of ATLAS (bothe would make great animated movies)
Silver Surfer (Galactus, and various other space characters)
Marvel's What If (Where Marvel animates 3 What If stories, with narration by the Watcher. These stories range from known Marvel characters like Spider-Man to fairly unknowns. Each could have different animated styles as well as different writers, and could have many sequals. Could even have one, every so often, a "What The" story after or inbetween two What Ifs.)
Team Ups (Hulk meets Spider-Man, Punisher versus Daredevil, X-Men and Spider-Man, Wolverine and Captain America, X-Men and Avengers and Fantastic Four versus Galactus. Team ups that we know can't happen in live action movies.)
