How to cut out 3 days from this Prague-Salzburg-Munich-Berlin Itinerary?

Cut Salzburg, Munich, Fuessen. That takes out 6 days. Now add 2 days in Nuremberg (hiking in the Frankische Schweiz), and one more day to Berlin, since your old itinerary short changed it with only 1 full day.

Füssen is the outlier and your time allotted to both Munich and Berlin is too short. Given that you are departing from Berlin, I'd take out both Füssen and Munich. If you feel that you need to see Salzburg book a cheap flight to Berlin well in advance. Otherwise the least stressful variant might be to concentrate on Prague and Bohemia (day 1-5) and then backtrack towards Berlin, maybe with a stopover in Dresden (day 6 afternoon /7 morning). That would give you three days for Berlin, which is barely enough.

If you had asked before purchasing air, I would have said to drop Berlin and fly out of Munich. With a commitment to fly out of Berlin though, I would agree with others to cut Fussen and maybe Munich too so you have more time in Berlin. It's always tough when you have to cut things you really want to see.

Unfortunately, you have a tough itinerary to "fix." Have you heard of the movie A Bridge Too Far? I think we could call your itinerary "A City Too Far." You would be in great shape if you were flying out of Munich.

The challenge with the fixes above is that you have a long travel day if you are traveling by train. CK to Nuremberg is 6.5+ hours. CK to Dresden is around 6 hours. Even CK to Salzburg is around 5 hours. That's close to losing a whole day to travel by the time you add breakfast, checking out of one hotel, local transportation and checking in at another hotel. You can drive it, but there will likely be an enormous drop off fee if you pick up a rental car in the Czech Republic and drop it in Germany.

I'll throw out one other option that may or may not interest you but dramatically shortens travel times. You could start at Prague and then head north, getting your small town/nature needs filled with a stop in Saxon Switzerland. Something like Prague x 3 nights, Bad Schandau or Königstein x 3 nights (1.5 - 2 hr train time; both on the Dresden S1 line so easy access to Dresden), and then Berlin x 4 nights (3-4 hour travel time). You would have to save the Alpine scenery for the next trip, but I think you would probably enjoy it more on a trip that gave you more time to take it in.

Thank you all. We are definitely cutting back to a more manageable and relaxed pace trip, even if it means leaving Munich and Bavaria until another trip someday.

Right now, we think we'll take advantage of flying to Prague and concentrating on the Czech Replublick, taking a lot of what you all said into account. So our itinerary is shaping up more like:

Prague 3-4 days
Southern Bohemia/Cesky Krumlov - 3 days
Berlin - 3 days

What's the Best route from CK to Berlin (bus to Prague, then train, perhaps?)

My suggestion would be to go to CK and Bohemia first and then return to Prague and train from there to Berlin. From CK to Berlin would be about 8 hrs - either bus and train or just train, while train from Prague to Berlin would be closer to 4 hrs.

Cut out CK and Füssen, add that time to Munich and Prague.