I really like the way they have things setup in the Avengers animated series, because Iron Man is leading but of course he's wet behind the ears when it comes to leading things, including Stark Industries. That's the perfect portrayal for the movie.
I don't think having Tony lead is as out of left field as having Wolverine lead the X-men as he did in X3. Tony has always been a key figure in Avengers and was a founding memeber (Cap was not).
But I think the best way to look at this, as some one mentioned is like Star Trek with Kirk, Spoc and Bones. All three leading characters.