Based on some posts around various internet blogs, I have found that there are a fair amount of people who don't like the way Marvel 'shoehorns' story lines into their movies so they can bring everything together into one universe.
I really don't understand why the crossing of so many films is viewed as a bad thing. Hell in the comics Iron Man only had 6 issues of Tales of Suspense before he started pulling double time in the Avengers. Don't get me wrong I love it when Iron Man is fighting villains alone, but most of my favorite Iron Man moments aren't even from issues titled 'Iron Man'.
This is especially true in recent years of comics. You can't go two issues without heroes tripping all over each other and showing up in pages not exclusively for their adventures. One of my favorite scenes from the comic world is a simple holographic chess game between Reed Richards and Iron Man. Or during Stark Dissembled when in order to 'reboot' Tony Stark Thor had to strike Mjölnir against Captain America's Shield to reboot the repulsor in Tony Stark's chest.
Iron Man, Captain America, Thor and Hulk have great stand alone stories, but to say it is a bad thing that we ignore around half of their comic career just because we don't want a mixing of movie franchises is a bit much. So much of their respectful lore is amplified by the Avengers and in some cases made much better. Seeing Tony try to wrap his head around the mysticism of Asgardian magic or watching Captain America and Iron Man fight over the Super Human Registration act is part of their comic book history so why should the films ignore that?