Whatever cities you visit, you will enjoy yourself I think. As others have stated, suggestions may be based on your interest.
In Munich, visit the Deutches Museum, watch surfers in the English Gardens and then stroll around (be advised, some of it is clothing optional),and while it will be a madhouse during Oktoberfest, eat and drink at the Augustinkeller.
We had luck with award nights at the Aloft near the Oktoberfest grounds. Good location.
As far as the rest, I second Berlin. Amazing city.
Also, make sure you visit a small town. Find the town center, find a bar or restaurant, have a drink and some food.