2 weeks in Bavaria region

Hi, Together with my wife we are thinking of going to Bavaria from September 20th up to 6th October. We like to see museums, landscapes, palaces/castles and nice towns. We will fly into Munich and out of Munich, so I prefer that the last base will be Munich, during Octoberfest. What other 2 towns/cities do you suggest that I can base myself in apart from Munich? Important that from these bases I can reach other towns or sightseeing for day trips using trains or public transport. Any help please?