Germany itinerary suggestions and how long for Munich?

Great itinerary with a nice blend of urban and non-urban places. Did you consider adding Dresden/Leipzig / medieval Gorlitz midway between Prague and Berlin? Another medieval stop similar to Ceske Krumlov is Tabor, midway between Krumlov and Prague.
Historic towns to hit (and your cruise may be stopping at some) include Mainz, Koblenz, touristy but beautiful Heidelberg.
Bamberg is a great historic town, and you have it included already.
Munich and Berlin have incredible museums of every category. You could probably shave a day off each of them in addition to one night from Bamberg and possibly scratch Rothenburg (it was almost completely rebuilt after WW2) if you wanted to see more highlights.

I like Munich very much,and staying there for 6 days is no hardship for me ;-)

Lots of interesting museums,great food (the best in Germany for me),plenty of good wine as well as beer.And the city is surrounded by great countryside,mountains and historic towns/villages/other sights.....

I am not a great fan of Stuttgart and would cut it down to include Strasbourg, but it is just my personal opinion.
It is of course possible to stay in Potsdam and go by train to Berlin every day, but what is the reason behind? Unlikely some other European destinations it is not a problem to get a hotel room in Berlin during summer months.

Not a good idea for me either..of course it is possible,but no point IMHO.

Berlin is more interesting,has a lot more to see and is not more expensive than Potsdam..why travel in and out every day?

You don't need three days for Stuttgart. Porsche and Mercedes museums need together one full day and the town is good for one more day. The southern surrounding is very nice and has some pretty villages like Tübingen, Hechingen and if German / Prussian history is your thing go to visit the castle Hohenzollern nearby. I would also skip the night in Rothenburg o.T. - if passing by a half day for sight seeing is enough. Same for what concern Potsdam it's dead in the evenings, stay in Berlin.

instead of three bases in the SW, you might consider just two (e.g. Meersburg and Tübingen) or even just one, and do daytrips to the other places - they're all conveniently enough connected. as for Stuttgart and surrounds, I recommend searching the archives with the following parameters (thanks, marcopolko)

though I realise that cars (and driving) are part of this trip, personally I can spot little value in having a car beyond Cologne - long and boring drives on motorways that are known for heavy traffic. no use for a car in Berlin itself. if still determined, I suggest swaying from the more direct A2 via Hannover to the less busier A44/A38 with lots of lesser known gems.

and fully concur with the others, there's no gain in staying in Potsdam if your destination is Berlin.

destroyed in the war/rebuilt wouldn't be a decisive factor for me, since it applies to almost all places in Germany anyway.

One other thing you have to make sure that your car is allowed to enter Czeck by the rental company, some don't allow any of their cars to go there, others only high end cars, so make sure before you book anything.

Vielen dank! Thanks so much everyone for your helpful replies! I'll definitely take them all into account when booking and planning.
Sue :)

I'd lose the car in Cologne and either fly or take the train to Berlin - you definitely won't need a car whilst running around Berlin. The rest of the itinerary is fairly OK.