1. There was no Han Solo-type (everyman) character. Everyone was way too uptight and it showed.
2. Anakin was extremely unlikable. The Clone Wars' biggest surprise was how they made him actually a heroic guy. They played up his pilot skills and I can see why Ben called him a cunning warrior.
3. The decision to go away from 35mm to digital. Digital will never have the great feel of film.
4. Lucas at that point had surrounded himself with yes men and he had no one to tell him some ideas were crap. It was less a collaborative effort. Plus I think his brain had gone to mush as a result of spending 15 years raising kids.
5. George Lucas should never try to write love scenes. He doesn't strike me as the romantic guy.
6. Turning the Jedi into monks instead of samurai.