The problem with Malekith was not that Marvel didn't like him. The problem was that Marvel has a raging ***** for Tom Hiddleston's portrayal of Loki, and cut a bunch of character development and characterization for Malekith in favor of having Loki ham it up onscreen some more.
Christopher Eccleston is on record saying there were a bunch of scenes that fleshed out Malekith and gave him some more nuance and motivation that ended up on the cutting room floor.
You had a similar problem with Iron Man 2. Whiplash had a bunch of scenes meant to humanize him and make him seem more sympathetic, and they ended up falling by the wayside because Marvel wanted to cram Black Widow and a subplot about the Avengers into the movie.
The problem is less that Disney hates villains and more that Marvel consistently tries to include too much stuff in their movies.
No. Marvel crammed the War Machine storyline at the last minute when Cheadle was cast and that was the reason Whiplash got the shaft.
I remember Feige saying that Whiplash was going to have numerous suits to compete with Iron Man, instead we ended up with the race track suit and some generic, forgettable suit at the end and instead of Legacy Studios and ILM having to work on Whiplash Mk II and III armors like Feige had said, they had to work on the Mark II Iron Man armor (again) that Rhodey steals and the War Machine armor. Then there was Mickey Rourke saying how excited he was to play Vanko and that he wasn't going to be a one dimensional villain, how he visited Russian prisons, but instead his scenes got cut for the War Machine subplot.
Apart from Iron Man, all the promotion, commercials, toys, merchandise, posters were for War Machine, not Black Widow and especially not Whiplash.
Yes they were trying to promote an Avengers movie, but it wasn't with Widow, it was with War Machine and to show audiences that Iron Man can be a team player. Thus Vanko got the shaft big time.
This whole thing about Black Widow taking up time and subplots is nonsense, she mainly shared time with Pepper Potts and had ONE action sequence. Not once did she have a side by side action sequence with Iron Man. War Machine was the one that took precious screen time, sfx, visual Fx, action scenes, promotion, etc away from Vanko.