They may have changed some storylines, but 99% of the time they've tried to be pretty true to the ethos of the characters. For instance, they killed cyclops, but he was still cyclops.IN THE COMICS.
Don't you think it's pretty clear that they will deviate from the comics for the Avengers movie? They did it for X-Men, why not The Avengers? This is the danger you get into when trying to look at a multiple hero movie with already established individuals.
And really, there is nobody out there that could portray the kind of authority needed to lead RDJ, Ed Norton and Samuel L. Jackson.
Then again, remember, RDJ WAS led by Ben freaking Stiller of all people at one time.
You can't have Captain frigging America in a movie and not have him be the most charismatic leader (whether or not it's in name) on the screen. At the very essence of Captain America is that even anti-heroes like Punisher and Wolverine stand in awe of the man and what he stands for.
So, yes, while I think both BIM and I understand that this is a different genre, I don't think they're going to have Captain America take a back seat to Nick Fury in his own movie. They might not be able to pull it off if Evans is wearing the uniform, but they'll try.