If you are interested in war history, here are my recommendations for your time in Berlin:
1) Deutsches Historisches Museum: Excellent display of German history. Gives an indepth context of German history and day to day life leading up to, during, and between both World Wars. I ended up going back here for a second day.
2) Topographie des Terrors - An outdoor display set in the former headquarters of the Gestapo. Excellent source of Third Reich history.
3) If you are also interested in Cold War history, check out the Museum am Checkpoint Charlie (history relating to the Berlin Wall, escape attempts, etc.) and/or DDR museum (Did not go here, but seems to focus on daily life in East Germany) but not until after the DHM.
I agree with other posters here in that Frankfurt can be skipped. Go to Munich or spend two more days in Berlin. Berlin is huge, but there is lots to see and it is really easy to get around by subway.
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