After traveling to Germany many times in the past eight years, I have to say that my favorite time is the fall. Not simply because of the Oktoberfest, but mainly because of the repercussions of that festival. In Bavaria especially, the fall is a very festive time of year with each local town having their own celebration. The weather is usually fantastic with nice days and cool nights and occasional rainfall, this is truly the autumn at its finest. You will definitely experience a true fall with the plethora of colors that will abound from the turning trees.
The mood of the people in the fall though is what I think draws me to Bavaria in the fall. Everyone is joyous and they seem to pass that sentiment along to people. With each fest comes great food and special fest bier, especially for the occasion and the celebrations take full advantage of the beautiful outdoors as well.
For a vacation that will leave you completely refreshed and rejuvenated, I suggest trying out Bavaria in the fall. I believe that you will truly enjoy the decision.
Oh, and of course there is that big celebration in München also!