That's a lot of travelling! I haven't been to every city on your itenerary, but I can share some experiences:
If you have the inclination to want to see the BMW factory in MUC, then by all means see the Deutsches Museum. This is the German science and technology museum and is huge! If you don't tire easily, you could easily spend the full day there. It's not that far from the, er, nightlife either.
BRU is a "nice" city, NATO headquarters and all that, but I wouldn't call it exciting. Kind of like the Toronto of Europe.