My daughter and I just returned from Germany. We started in Hamburg, went on to Berlin and Dresden, and finished up in Munich. I wanted to share our experiences in hopes of helping someone.
Flight- if you are flying Lufthansa, the premium economy tickets are well worth the price. Be warned that if you upgrade at the airport in Frankfurt, you will be sent upstairs to buy the new ticket. Then you will go back down stairs to check your luggage. If your luggage weighs too much, you will go back upstairs to pay for the extra weight. We were relieved that our luggage weight was ok. As it was, we got there two hours before our flight, and barely got on board in time. The security checkpoint moved slowly because of the large numbers of people. So if you need to do anything special, add an extra hour to your arrival time.
Train- We bought a flex pass. Our travel agent bought us special tickets for two of our ICE train trips. NO ONE EVER EVEN LOOKED AT THEM. Rick says you need them too, but I don't think so. We got on other ICE trains without any extra fees. We took an EC train (Czech Republic) between Berlin and Dresden. You pretty much have to have a reserved seat for them. We spent the entire trip in the dining car. Also, look not only at the schedule for your track number, but also look at the picture of the train layout. It will be at the arrival/departure track. We found it easier to stow our luggage at the back of the car. Once we figured that out we got on the back entrance when boarding the train.
Hamburg was great. Not many tourists, but lots to see and do. Everyone was friendly and most spoke English. We stayed in the Soffitel, and it was perfect.
Berlin- We loved Berlin. So much to see, and history to experience. We stayed at the Arcotel J F, and it was nice. We took a taxi from the Hauptbanhof.
Dresden- Our hotel - the Steinenberger- was near the castle and Frauen Kirche. Perfect location. They didn't have wash cloths in the bathroom, but the room was nice. We loved Dresden. It was a quick trip on the way to Munich, and we wished we had more time.
Munich- We stayed at the Hotel Eden Wolf. Also a nice hotel. It was conveniently located across the street from the Hauptbahnhof and down the street from Marienplatz. Munich was our least favorite city. It was more crowded and felt touristy. We took a tour to Lindenhof, Oberammergau, and Neuschwanstein. Lindenhof was a beautiful palace, and well worth the trip. We had about 20 minutes to shop in Oberammergau, which wasn't near enough time. Neuachwanstein was beautiful, but the climb was a killer. If you aren't fit, do yourself a favor and take the bus up. I consider myself reasonably fit, but it was a long uphill climb. Follow Rick's advice about tickets and entry.
We took the train from Munich to Frankfurt for the flight home. We spent the night at the Steinenberger Airport. If you spend the night in Frankfurt before your flight, go for the Sheraton. The Steinenberger was beautiful (no washcloths again), but the Sheraton is attached to the airport which gives you more time to get through customs, etc before your flight.
If I had to do it all again I would limit myself to two major cities to reduce the time spent on the train.