As for the emperor I don't think he is the main villian, Vader is IMHO.
The main villian is not determined by where they rank in the badguy infostructure, its how important they are dramatically and who has the most personal and powerful conflict with the main protagonist.
Infact often in action films its actually the second in command badguy who proves to be the true nemesis of the hero. This was often done in Bond films and other action pics.