Re the magic issue and audiences acceptance thereof - a couple of years ago, people were voicing the concern that Thor would be a hard sell, with his Norse Gods etc, but that worked out all right.
That's an illustrative point, though, because the movie went to lengths to emphasize that it wasn't magic or gods but aliens. Everything from the beginning intro to the "sufficiently advanced science is indistinguishable from magic" line just wanted to harp that point so the audience wouldn't reject it.
I think they can easily do that here. Advanced, unexplainable alien technology seems to be the rule of thumb for Marvel movies. After that, they can have whatever magic they want.