UPDATED! Jon Favreau has told Marvel he will not be helming Iron Man 3. That's according to Vulture, whom posted that an insider in Marvel informed them. As it's all he-said, she-said, take this with a grain of salt, but I'm putting my money on it being true. After Iron Man and it's sequel, Favreau began to tally up potential projects (Cowboys & Aliens, Magic Kingdom) so it's not surprising to me that he's walked away. Vulture have no solid information as to why he is choosing not to return but they're speculating that it's because of he's asking for too much. Personally, I get the feeling the relationship between Favreau and Marvel is iffy, at the best of times.
UPDATE: Favreau himself confirmed the news today via Twitter. He writes, "It's true, I'm directing 'Magic Kingdom', not 'Iron Man 3'. I've had a great run with Marvel and wish them the best." In a new interview with LA Times, Favreau also stated it has nothing to do with money.