I don't think so, although it might be in his Essential Cinema list. He did include Panic in the Streets, which although I wasn't a huge fan of Kazan considered it his first film that came off exactly as he intended. As far as the AFI, because the list(s) are voted on by a board of nearly 1500 people you can't be surprised that popular favorites will win out. Ask the National Society of Film Snobs/Critics to do the same list and rest assured there'd be some unconventional choices.