I think Marvel's actually done a pretty great job of integrating the movies, visually and thematically, in an auteurist sort of sense, into one cohesive way of being while at the same allowing room for directors to play around. They impose a framework, which is logical, but they do not stifle the creativity of the directors they invite to play around there -- at least, not really going by the movies themselves. The behind-the-scenes stories suggest otherwise, but I dunno.
We got what was pretty clearly a Johnston movie with Cap, and Thor is very Branagh. Favreau doesn't really have an aesthetic of his own, as much as I think he's a fine director, but just by casting Downey and giving them both the freedom to improvise almost everything daily (at a time when the company's whole position, movie-wise, was much more tricky) I think they showed that they know the importance of creative vision, but also know it needs to have some logical limits to make the machine run as they need it to.
I do get your complaints, though, Gabe, and Feige definitely has a share of input that is in many ways creative and could be considered an infringement on his directors. We're not going to get something as distinctive as The Dark Knight out of this deal. But I think I like Thor and IM and even Cap a little more than that movie, which I don't often return to and do think is somewhat overrated, so it's not something I totally have a problem with.