The Altes Museum is under renovation and we actually saw much of its Egyptian collection in Munich (but not Nefertiti).
The Pergamon was WONDERFUL can be like no other museum in the world. Sadly I only had 2 hours there. It is one of those museums I'd happily spend 3 days in.
The huge reconstructions inside the museum were very impressive.
The European Trains were great: clean, on time, and I didn't have to worry about parking or driving.
Munich seemed too arrogant but Leipzig was very nice. Rothenburg Ob Der Tauber was a joy and Amsterdam is just a wonderful city. Everything was very expensive.
Thanks for the advice everyone!