Germany and Switzerland, what to do, what to do?

Something like this perhaps over 3 weeks ...

Berlin (4)
Dresden (2)
Wurzburg & Rothenburg (2)
Heidelberg & Rhine (3)
Lausanne (1)
Berner Oberland (3)
Luzern (2)
Munich & Bavaria (4)

Some architecturally fab smaller cities in the eastern part of Germany for your consideration: Quedlinburg, Erfurt (near Weimar), and Gorlitz. I know there are many other lovely places, but I unfortunately haven't seen them yet.

While in Berlin I took a nice change-of-pace day-trip to the Spreewald. It's a marshy area where you can walk, rent a canoe/kayak, or ride in a somewhat larger boat. I don't remember whether biking was an option. I took a train to Lubbenau, which seemed to be the center of the tourist activity. There's about a 1-mile walk from the RR station to the main square. Boats depart from near the square.

Rick's newest Switzerland tour itinerary debuted this year and a new Germany tour will go on sale by the end of August, with the rest of 2017 departures .

There are basically three regions you could visit between Berlin and the Amerian sector (Bavaria):

Harz mountains
On the map they are a bit out of the way, but several trains to Munich take this route.
The Harz mountains are Northern Germanys highest mountains. At the foot of the mountains are several medieval towns full of half-timbered houses, among them two World Heritage Sites (WHS). Some of these towns are connected by the biggest steam train network of Germany, and one of the routes goes up to the highest peak, the Brocken.

Saxony
Way too often Dresden is only a short stop between Prague and Berlin, but Dresden is probably the best base for day trips after Munich. You can see beautiful preserved towns (Bautzen, Görlitz, Pirna, Freiberg, Meissen), see fortresses and palaces (Königstein and Pillnitz), hike in Saxon Switzerland (most beautiful mountains of the country with the Alps), see cute wine villages (Dresdens suburbs) or visit Germanys Christmas country (the ore mountains). You could also rent a bicycle and bike along the Elbe, or rent a boat and cross Saxon Switzerland from the Czech border to Pirna for example.

Thuringia
The green heart of Germany, with dozens of tiny towns which once were capitals of equally tiny duchies, that's why every tiny town sports a huge castle. The highlights however are Erfurt, the capital of Thuringia with one of the biggest preserved old towns of the country, Weimar, a beautiful small town incredibly important for the German culture, and the Wartburg, Germanys historically most import castle.

Other routes
You could also follow the most direct route. On this route you could see Wittenberg (Luther, WHS), the Dessau-Wörlitz Garden Kingdom (WHS), Dessau with the Bauhaus buildings (WHS), Leipzig (Bach) and Naumburg with the most famous statues of the Middle Ages.

Around Berlin
Since you mention that you like to be active: Potsdam, which you will hopefully visit, is much more than just Sanssouci. The city is surrounded by other royal parks and lakes, and renting a bicycle is a great way to explore the city.
And the Spreewald, already mentioned, is a wonderful day trip too. You can do a tour on a punted barge, rent a canoe or a bicycle, or simply hike. But avoid the weekends! This area is very popular among Germans, who like to spend several days there.

Thank you all! I appreciate your responses, it really helps!