First Time Concerns

The German train system is wide-ranging, runs frequently, and does not tend to require reservations, which all contribute to it being quite manageable for tourists. See Ricks' German rail page for info about both the German rail pass (with two-passenger discount and hop-on convenience) and point-to-point train tickets (with advance-purchase discount available if you're ready to lock in dates and times).

Info in English is available in stations, since English is the official language of the European Union. We use the English version of the German railway site to get train schedules for all of Europe; see How to Look Up Train Schedules Online.

The cities you listed all have reasonable amounts of English available, so that shouldn't be a problem. And as Laura said, the train system is easy. If you can lock in to non-refundable and non-exchangeable tickets (or can accept significant restrictions on those actions), you can pre-book tickets that you print out at home, at a SIGNIFICANT discount. Or a German Rail pass may work better, since you don't have to commit in advance. Or, if you're taking only a few trips, you may elect to buy full price tickets at the station for greatest flexibility. All methods work well for certain situations - your choice.

For potentially crowded trains, I recommend reservations; they are optional on all but a few German trains, but they are inexpensive, and very handy if you have luggage (since you get a seat and space above it to stow your stuff, instead of sitting on your suitcase in the aisle of a full train).

As always, the larger the city, the larger and potentially more intimidating the train station (Berlin's is huge and has tracks on multiple levels, although it is very clearly signed). Arriving 15-20 minutes early is recommended, more if you want to buy some food, use the toilet, etc. But you can arrive until they close the train doors (about a minute before it actually leaves) and still make your train. At each station, there is a reliable taxi rank, in case your hotel is far from the station or you do not want to schlep with your bags. Once you've stowed your bags at your hotel, the mass transit in German cities is excellent, so you only have to take a taxi if you want to.

Rick's Germany book covers the cities you mentioned and will have lots of logistical help (where to catch which bus, etc), but you may want to look at other books as well; the consensus is that his coverage of Germany is spottier than of some other places, and, more than in some other countries, his likes and dislikes are not shared by everyone.

Here's my report of my trip from 2012 with my mother, in which we visited Berlin, Dresden, and Goerlitz: http://tinyurl.com/9woj9zo

Our very first trip to Europe some 17 yrs age we flew into Paris and after 3 nights there we took a night train to Frankfurt and traveled by train for two weeks in Germany. My husband was very unsure of the whole thing and very nervous before that first trip - we had everything planned out and reservations everywhere. We have since been back to Europe 8 or 9 times - Germany at least 5 or 6 - we usually travel by train and love it. The German train system is so user friendly and the wonderful German people always happy to help. Most if not all of the stations have excellent signage in English or pictograms. I am certain you will do fine.

While I agree with much above, and signage everywhere is easy to understand especially with the pictographs, I have never heard that English is the official language of the EU. Don't tell that to the French, or the Germans, or the Italians for that matter.

Don't expect everything to be in English for your trip, nor that everybody will speak English, but many can - at least some - and your trip should be loads of fun!!

I've found that travelling in Germany tends to very easy, and I seem to get back there on a fairly regular basis (I'll be there again later this year). The German rail system (Deutsche Bahn) is one of the best in Europe, and their website has extensive information on trains all over Europe.

Regarding your concerns.......

• Language - anyone dealing with tourists will have some ability to function in English. Many (especially younger people) will be fully fluent. Of course, it's possible to find people in smaller shops that may not be able to speak English. I don't speak German, but can usually manage quite well. As with any country, it's always polite to know a few of the usual greetings - good morning, good night, please and thank you, etc. You might find it helpful to pack along copies of both the Germany guidebook as well as a German Phrasebook (both available on this website). The Germany guidebook has some language information, but the phrasebook provides more detail. The Guidebook also has an enormous amount of good information to plan sightseeing.
• Train system - as mentioned above, it's very easy to use. You can plan out your journeys on the bahn.de website. I usually try to pick trains with the shortest travel times and minimum number of changes. Note that many cities have more than one station, so you'll need to know your departure and arrival stations when buying tickets. When staying in cities, the local transportation (S-Bahn, U-Bahn, Trams) work well. When buying tickets for day trips in Munich, you could use the helpful EurAide office, which is located at Desk 1 and has English speaking staff (on the left) inside the Reisezentrum (ticket office) in the main station (Hbf). As you're experienced travellers, I'm sure you'll figure out the trains very quickly.

The Guidebooks have good information on hotels in each city. When is this trip taking place? I'd suggest pre-booking hotels if you'll be travelling during peak travel times. The group here will be able to provide lots of suggestions for hotels once you've got the details worked out.

Gute Reise!

It already gets much easier, and cheaper, if you book the train tickets in advance:
http://www.bahn.com

Between the big cities you can get tickets for the high speed trains (ICE) 90 days in advance, AFAIR. You just have to print them out. The only downside is that you have to use the booked train.
For day trips you can use the so called Länderticket, which you can print out too:
http://www.bahn.com/i/view/GBR/en/prices/germany/laender-ticket.shtml

BTW: there is a lot to see in Northern Germany, it's a bit odd to ignore it and cross the whole country instead. Here is a map of Germanys highlights according to Baedeker, Germanys most popular travel guide:
Highlights of Germany

Hi,

If you are experienced travelers, then traveling in Germany is easy when following the train and signage systems. Of course, one can get around in Germany pretty easily without knowing the language especially as regards to the big cities. But being able to read the language allows you to get much more out of the trip. Good that you've set aside several days in the Berlin and Munich areas I'd do the same. What do you plan on seeing and where specifically? No, to hotel hopping every night, that gets tedious quickly.

To echo Ken, it's polite to learn a few words and phrases in German to use when you greet store employees, ticket sellers, etc.; or if you have basic questions. Some words and phrases include:

Hello / Goodbye / Good morning / good evening
Where is the bathroom / train station / the X museum / etc.
How much does this cost?
Please / Thank you / You're welcome
I would like to order the X dish (food words and phrases, so you know what you're eating and drinking)

You can pick up some language guides from the library or look at some in a bookstore.

The only time where it can be hard to find people who don't speak minimal tourist English in shops and restaurants can be in parts of the old East Germany (the people over 35 learned Russian in school instead). Rick's phrasebook is very useful in decoding restaurant menus in places that don't have an English language one, which many do.

It's a place where it's pretty easy to muddle through with a lot of Dankes and a good attitude.

Hamburg is the second largest and most beautiful German city. It's packed with sights and history. As a city it is much nicer than Munich.

"(the people over 35 learned Russian in school instead)." As I learned recently, it would be more accurate to say "they attempted to teach them Russian in school". Actual Russian fluency in the DDR was extremely low.