Acting is a job like any other. Sometimes you enjoy your job and sometimes you end up having to do things that you'd rather not. Christopher Eccleston may be best known as the man who brought Doctor Who back from the dead on television, but after that, he made a pair of tentpole movies in Hollywood, and, apparently, he absolutely hated making them both. According to Eccleston...
A lot of actors would be happy with a big blockbuster movie role. Generally speaking, they pay really well. However, Christopher Eccleston doesn't feel that the money was worth it. He goes so far as to tell the Guardian that taking those jobs for the paycheck was him "being a whore." There's really no way to sugar coat that. Eccleston really didn't like making those films. While he doesn't seem to think that the paycheck was worth it, at least he got the paycheck or there wouldn't have been anything redeeming about the experience.
While Christopher Eccleston doesn't go into specific detail regarding what the problem was with G.I. Joe: The Rise of Cobra, where he played the role of Destro, or Thor: The Dark World, where he played villain Malekith, it seems that being big budget blockbusters wasn't the sole problem. He apparently enjoyed his role in Gone in 60 Seconds from a few years earlier, so it isn't just Hollywood he has a problem with, either.
It should also be pointed out that Christopher Eccleston isn't blaming anybody but himself for the roles. He took the roles and seems to accept responsibility for them. It just seems that if you're looking forward to seeing the former Doctor on the big screen in a major Hollywood blockbuster in the future, those odds are probably fairly low.
For what it's worth, it's somewhat understandable that Christopher Eccleston didn't love those particular roles. Nobody is going to include Malekith on a list of "Best Marvel Movie Villains." He's more likely to show up on the list of characters whose names you forgot. Nobody is going to call G.I.Joe: The Rise of Cobra the best movie either, though it's still possible to enjoy yourself even if the movie isn't great. That didn't happen here.
It's too bad that Christopher Eccleston had such bad experiences with these films. When you don't enjoy your job, the job just seems longer. Hopefully, he'll find roles going forward that he at least enjoys performing.