Consider taking The Romantic Road (Wurzburg to Garmisch/Fussen),
The first visitors were friends and families of the American soldiers stationed in the large bases in Bavaria and Baden-Württemberg but the idea of the trail from Würzburg to Füssen soon became wildly popular.
It's not too hard to see the reason for the popularity - despite the modern roots of the idea, the tour combines the historic cities of Würzburg and Augsburg with the three medieval walled towns of Rothenburg ob der Tauber, Dinkelsbühl and Nördlingen, and then finishes off with the tourist highlights of Neuschwanstein Castle and the Alps.
The road has several walled medieval towns and small cities as well as larger cities like Wurzburg and Augsburg.
Then spend some days in Garmish, see the famous castles, go up the Zugspitze (tallest mountain in Germany). From there, you could cross over to Innsbruck, Austria for a few days then head to Salzburg, or go directly to Salzburg. After a few days head to Munich, stopping for a day in Berchtesgaden. Do the Eagles Nest.
Spend some time in Munich, then take in Regensburg and/or Nuremberg and Bamburg.