Germany

I'd prefer Munich. I don't particularly like large cities. Munich doesn't feel that way to me. Plus there is so much to see in the surrounding area, far more than you can see in 3 days.

But my decision would probably be based on which city was closest to where I was entering Germany. Might as well minimize your travel time (and expense) to maximize you time there.

Berlin is large. modern, trendy, and a bit edgy. It is full of Cold War sites and moving WWII memorials. Having visited in the Cold War days, where we walked through Checkpoint Charlie to visit the East side, I was anxious to return after the fall of the Wall and walk through the Brandenburg Gate. Now that I've done so, I'll keep returning to Munich, which is smaller, friendlier, and has my favorite park (Englischer Garten) and favorite museum (Deutsches Museum) in the world. Munich is a walking city and a real pleasure to visit. Berlin is fun and exciting, but too busy for me.

You, of course, might have completely different tastes, especially if you are younger.

Berlin, more to see and do and lots more fun.

I haven't been to Berlin, but Munich has the advantage of being near the Alps. Lovely.

When you get to Germany, I hope you have three full days to spend in your choice city. The best city, as you say to visit, is Berlin, no doubt about it...vibrant, exciting, fascinating, great walking city too, and it's cheaper than Munich when it comes to accomodations.