It's actually Jon not John and I believe he will return as director if he's not locked up already.
Everyone expected Bryan Singer to do X3, but he ended up getting kicked out. I just hope that doesn't happen to Favreau. He was the main reason along with RDJ that the first movie was as great and it was. It would be a tragedy if Marvel cheaped out and got someone like Ratner to do the next movie.
Also I'm still a little worried about studio interference. Raimi gave Sony two huge hits with the first Spider-Man movies, but they still forced him to put in Venom in the third movie.