The issue of brand confusion should not be overlooked. However, unlike the Disney-Pixar relationship, which was instantly solidified by Pixar branding becoming Disney-Pixar, we have not seen similar moves regarding Marvel. Yes, there is merchandise in the parks and the Disney Stores, but that is not much in the grand scheme. Yes, Disney marketed and distributed The Avengers, but Disney's name does not appear on any marketing materials or before the film, just a single line of text at the very, very end. We also have not seen even meet and greets at the parks, despite them continuing for other releases (see Merida from Brave).
Iger's words indicate that he would like to accelerate the establishment of a Disney-Marvel identity. I am starting to think more and more that it is Marvel that is resisting Disney's desire to more closely relate the brands. Iger seems to almost bordering on the thought that "content is content," where the people at Marvel could better see the different tones between the Disney's brands and Marvel's. Supposedly the Marvel executives were rather well invested in their company, which translated to so decent chunks of stocks in The Walt Disney Company. The success of the Marvel Cinematic Universe, as we are seeing right now, is something Disney wants to see continue, and alienating Marvel's key creative personelle could be tantamount to pushing out a group almost equivalent to Pixar's "brain trust." Disney spent $4 billion not just to acquire the characters, but also the people who have been at Marvel and turned around the company's fortunes, making it worth $4 billion.