I think Lynx makes some good points. We might disagree on how much weight to give them and how much they impacted our enjoyment of the movie, but they remain valid points nonetheless.

1. Loki was a truly pathetic, ineffective villain. This is easily ignored in such an action-packed movie, but it remains true. In Thor, he did a lot of major trickster stuff that developed over the whole movie. In The Avengers... he tricked Thor into running into his cage. Yeah.

2. The early fighting between the heroes (thinking of Iron Man and Thor here) was embarrassingly fabricated. I would have liked some sign that Loki was magically causing it somehow (as I first assumed because it made no sense otherwise). I chalked this up to the movie being too fast and cramped to be developed properly.

3. The aliens just sort of happened. There was almost no development of this plot point. See #2.