I think it really depends on what kind of activities you like. If you like mountains, hiking and lakes, you should come to Munich and from Munich head to the Pre-Bavarian Alps that borders Austria.
If you like history, especially WW2, then definitely Berlin.
To be honest, Germany has many cities that are really interesting. From Stuttgart (Mercedes / Porsche), Munich (Mountains, Nature and BMW) to the Rheinlands (German wine). There is something for everyone.
Hope this helps!