Marvel Studios is notoriously tightfisted with the purse strings, but also with the creative strings. Whedon will presumably ask for more money to direct Avengers II, and perhaps more creative freedom. Favreau supposedly had to incorporate a lot of elements into Ironman II that he did not want, but which the studio demanded(which partly account for it being a step down from the first movie). I don't see Whedon giving up as much creative control as easily.
The combination of keeping costs down and maintaining creative control could very well get the Marvel execs to go for someone cheaper and more manageable. I think Brett Ratner probably has an opening in his schedule.