I had half-expected Moviebob to gush about this film, afterall it's stuffed full of stuff just for the fans of the comics. Don't get me wrong, it's a solid 7/10 film with superb moments (favourites involve Phil, Loki, infighting and all Iron man and Thor quips), but it has flaws.
As Moviebob said the story is secondary and slim. The opening leaves you feeling you've missed a film and is taken a little too seriously for all the silliness involves. Loki's CGI army has no backstory, a stupid forgettable name, and just show-up as faceless goons to fight. How they're dealt with is a plot contrivance followed by a magical killswitch that left me with the impression they had forgotten the army weren't robots.
Also, the extended action scenes get a bit physically exhausting after a while, but that may just be watching it in 3D.
The worst scene was Loki making people bow before him (kneel before Zod, etc) and one old man with a stereotypical Jewish accent disobeys him. Captain American then shows up and compares Loki to...well if you can't guess where this is going already, here's a clue: the scene is set in germany. -_-
It's testament to how good the film is that the main storyline could be so bad, but not detract that much...
EDIT: Did anyone ever say 'Hawkeye'. I heard a 'Hawk' and his regular name, but it seemed like it assumed you knew already...