I haven't been to the Museumsinsel since most of it has been renovated by now, but imho it's a must to visit, both by the architectual standarts and all the stuff that is displayed there. You really won't be dissapointed. It's not a UNESCO world heritage site for nothing.
The aviation museum in Gatow was already mentioned, Berlin Tempelhof may find your interest as well. It probably is the worlds most famous airport building, despite having finally been shut down last year.
Maybe you are also interested to get a tour of all what is left from WW2 and the NAZI era, including the remnants of the Führerbunker. Quite a few buildings already used by the NAZIs are still in active service by the german government, including the Bendler Block, where Stauffenberg was shot.
Finally, if you weren't in Berlin for two days only, I'd seriously suggest going to Potsam and make a visit to "Sans Soussie" residence, a highlight of Prussian origin. The gardens there are stunning.
Be as it is, Berlin has enough to offer to keep you on your feet for 4 weeks straight, so you will have to be very careful in chosing what to look at. You will miss great stuff no matter what you choose.
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