Why did anyone think he would be?
The only reason he was the villain in Avengers was so that they could claim it was true to the original comics as he was their first villain the team fought despite that...
a) The movie version of Loki is more sympathetic than the comic version which had those elements developed over time.
b) A trickster god doesn't suit the grander way the Avengers come together in the movie hence why it was Thanos orchestrating it.
I think it'll be fine to keep him in Thor movies as he's important to that mythos and undeniably suits it.
He's good in Thor but since then he's been annoying. He's a pantomime villain now. Laughable