That's a good point about Cap. But perhaps there's room for both. Cap is certainly "the people's Avenger," representing the little guy. Carol could be "the planet's Avenger," defending Earth's (and its inhabitants') very right to exist. Of course, that does overlap a bit with both Cap and Thor, but oh well. Still more of a role than token female.
I like the idea of Ms./Capt. Marvel actually having some authority on certain matters, as well as a contrasting leadership style from Cap's. The greatest of leaders have consultants/confidants regarding the areas in life in which they themselves do not have an expertise (see: Captain Kirk with Spock and Bones, and even Scotty at times). I could see Cap respecting Carol's knowledge/experience enough to delegate some responsibility/defer to her--and in doing so, the rest of the team (even the supergeniuses) would follow his lead.