Sources suggest that Marvel may have deliberately pushed the director away, as he cost more than it was willing to pay.
Jon Favreau, who directed the first two Iron Man movies, will not be returning to make the third, instead focusing his energy on the "Night at the Museum-style action adventure romp," Magic Kingdom. The news began as just a rumor, but Favreau later confirmed it via Twitter, saying that he'd had a great run with Marvel, and wished the studio luck for the future.
Sources suggest that Favreau's departure is the result of Marvel's insistence that, in the wake of the Avengers movie, Iron Man 3 should contain a number of its other superheroes. Some Hollywood insiders are theorizing, however, that this was a deliberate move by the notoriously frugal Marvel to provoke Favreau, who was thought to be a little but too expensive for the studio's tastes, into quitting the project. The idea that Marvel was pushing a very busy vision for the third movie aligns nicely with comments Favreau made earlier this month about how the script for Iron Man 3 would have to incorporate the events of Captain America, Thor and Avengers movies as well.
The worry now is that the Iron Man movies will suffer the same fate as the X-Men Trilogy: two good movies under one director, and then a much worse one under a second. This seems even more likely if Marvel is genuinely looking to hire directors based on price rather than ability. What's more, assuming for a moment that it wasn't just a ploy to get rid of Favreau, if Marvel really does want Iron Man 3 to incorporate all those other movies, that seems like a surefire way of getting a dense and confusing script.
Source: Bleeding Cool