How about Cap's mask?
Honestly the movie was so damn good that it didn't bother me at all, and truthfully it didn't look as bad as I thought it would. I do prefer his WWII costume from the Cap movie, I just think it looked more badass but this one worked as well.
Another thing that normally bothers me in comic book movies is the heroes being "unmasked" to much through the movies. That was not the case in The Avengers, when Cap was unmasked by the Skrull it came across to me as it needed to happen, so that the people around him that he was saving could see that he was a normal guy just like them. Also they rarely had Iron Man with out his helmet on and I dig the shots that are supposed to be from inside the helmet.