I agree with most of these questions. My main concern and issue I had was the Hulk. I loved the fact he was able to control himself at the end, but wish we were given an explanation as to how he was able to do so. It made me upset that Marvel just sort of glanced over that. Still, it was great to see the Hulk back in action as a true hero for once.
Another thing that bothered me, too was Thor's return to Earth. I definitely thought Marvel's decision to leave him in Asgard at the end of 'THOR' was due to some scene in 'THE AVENGERS' in which we saw him return using Dr. Foster's methods or something. Dark energy seemed to be a bit of a cop out. Loved the movie, but there were a few holes I feel.