I thought making Iron Man the leader of the Avengers was pretty conceivable. I mean, first of all, this is quite blatently made to tie into the film canon and so far things seem to indicate that it will essentially be Tony Stark's team (Fury approached HIM and then Stark sought out Bruce Banner).

Also, in the comics it always seemed to me that Tony was the one pulling the strings anyway. Cap may have been the field leader, but as long as Stark kept signing the cheques, the team was essentially his.

That said, the Iron Man cartoon still sucks.