I read in GQ magazine Francis had no intentions on doing Godfather 3. The decision was a result of the studio wanting to cash in on the success of his other 2 films. To me that's why the movie is subpar compared to the other two films. His heart was not in in the right place. Kinda upsets me. He could have went off and did a personal film, which he favors, but instead he waste that talent on GF3. He's actually directed some pretty crappy stuff lately but if you pay attention his name is attached to a lot of projects as producer: Lost in Translation (which his daughter, Sofia, directed) being among those.
I don't think we've seen the last of him directing and he will drop something amazing in a few years. Sofia is fantastic also. The Virgin Suicides is one of my favorite films.
During the GQ interview he discusses how he was asked to help with a script for Godfather 4, not direct, just lend a helping hand but the studio turned it down. He goes into details regarding the story premise - How it would be two parallel stories. The first occurring directly after GF2 and the other half concerned a less important character introduced in part 3.