I enjoyed the Avengers movie quite a bit, but I did have some problems with it, and one of them is Loki. In Thor, Loki was a complex, nuanced, somewhat sympathetic antagonist; in The Avengers hes just pure malevolence, which is less interesting.
Actually that was my chief quarrel with the second Hulk movie too. In the first Hulk movie (which of course isnt strictly part of the Avengers continuity, but the second Hulk movie picked up so many narrative strands from the first that its hard to treat it as purely separate either), General Ross was likewise a complex, nuanced, somewhat sympathetic antagonist, and one who was opposed to the human experimentation that led to Banners condition; in the second Hulk movie Ross is more straightforwardly villainous (albeit not completely so) and is actually carrying on human experimentation himself.