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The director of the first two films will not be returning
Jon Favreau will not be returning to the Marvel Universe for a third Iron Man film, Vulture reports.
The article suggests that the choice was made at the director's discretion and that he informed Marvel Studios of his decision this morning. Though Favreau's reasoning is purely speculatory at this stage, it is likely that the director simply wishes to pursue other creative ventures. With the upcoming Cowboys & Aliens hitting next summer and The Magic Kingdom in the early planning stages, Favreau should remain suitably busy for the time being.
This isn't much of a surprise. Marvel dictated to him a lot more in IM2. He probably was being told the what/how/whens of what IM3 would have to look like. I guess too much executive interference stiffles the creative edge. That or he just wants other creative challenges.