Saw the Avengers for a second time. I was one of three people in the theater. Obviously not as much hype. I saw the things that bugged me much clearer.
(Spoilers)
First of all the aliens just shut down after the bomb goes off. May not have been as bad if it didn't remind me so much of It-which-will-not-be-named. It just doesn't make a lot of sense. They're not robots. Maybe its a hive mind type thing, but I don't imagine it would just cause them to drop dead.
Smaller things are hitting them on the head to fix them. It's feels cheap but it's simple. Too much build up for the flying slug things that didn't really turn out to be much of a threat since they had exhaust ports.
The scene in which everyone is arguing aboard the helicarrier works much better now that I know that the staff is messing with their heads. I wish they dropped a line about it to clear up the confusion over whether or not the hulk is in control at the end.
But, All that said its still a fantastic movie. I love what Joss did with the characters. And the set up at the end is... Pchow. (Thats the sound of my brain exploding.)