Hi,
If you want to focus on war history, there is a lot to see in Berlin It all depends on how much time you want to devote to tracking down these sites, which means dropping some of the list above. . Forget Checkpoint Charlie, as suggested above. I agree with seeing Treptower Park to see the Soviet memorial and military cemetery. For the war sites I suggest the Resistance Museum, (Gedenkstätte deutscher Widerstand. ). It's located on Stauffenbergstraße, within walking distance from the HI hostel on Kluckstraße.
Another place on war history is the museum at Berlin-Karlshorst, the actual site where the Germans signed the capitulation with the Soviets the day after they had done likewise with the Allies in Reims. (They signed four surrenders in total in 1945). That museum shows the war in the East. Take S-Bahn 3, get off at Karlshorst, good signage along the way. The ack ack gun towers (Flaktürme ) still exist near Berlin Gesundbrunnen. Information on this can be gotten at the Tourist Offices...one is at Berlin Hbf on the ground floor, another is on the east side of the Brandenburg Gate at Pariser Platz.
If you want to see a battlefield memorial and museum, do a day trip outside of Berlin to Seelow (Gedenkstätte und Museum Seelower Höhen). That is worth your time and energy to see every single exhibit inside and outside, all the more if you read German, likewise with Karlshorst. Take the train from Berlin Hbf to Frankfurt an der Oder then transfer to Seelow. There are also Prussian-German military cemeteries, which are accessible by public transportation, depends on the level of your interest. I tracked down three of them, one was the British WW 1 cemetery.