Germany/Prague/Switzerland Itinerary...Help!

1. Probably not, as your itinerary includes Czech Republic and Switzerland.
   
2. 3 to 4 days, time to relax, get to know the area a bit and take a day trip out of town.
3. Can't think of anything to avoid.
4. Consider 4 to 6 hour stops in Dresden on the way to Prague, and Nuremberg on the way to Munich.

Look at flying in to Berlin and out of Zurich.
Nail down your lodging in Munich as soon as possible. Town fills up during Oktoberfest.
Consider taking a bus from Prague to Nuremberg/Munich. Quickest, cheapest way to go with an advance purchase nonrefundable ticket.
Get train schedule and prices (once you are 3 months out) at www.bahn.com
Edit- Mountains in Luzern area will put Black Forest to shame. Bavarian countryside easily done with a day trip from Munich. Use the Bayern Ticket for all day travel on the trains for about 27 euro for the 2 of you.

Is the Germany rail pass worth it?

No. Buy tickets in advance at www.bahn.de, that's cheaper.

How much time should we spend in each city?

Berlin 5 days, Prag 3 days, Munich 4 days, Lucerne 1 day. If you add the time you need to to pack, unpack, check in and out and travel between the cities you don't have time to see anything else.

What should we definitely see/avoid?

Definitely do a day trip to Potsdam from Berlin. Drop the Black Forest, because it's a detour, and Lucerne, if you fly out of Munich.

Any other locations we should try to see?

Yes. Instead of the Black Forest see Saxon Switzerland. The train from Berlin to Prague crosses these mountains. You just have to leave the train at Bad Schandau, take the next S-Bahn to Rathen (18min), cross the Elbe river on the reaction ferry, walk up the mountain and you stand on the bridge you see in the picture.

I'm not sure about the rail pass. I think we had one when we went on the Germany, Switz, Austria trip a few years back. I remember it took a while to coordinate the train schedule.

I would say the cities you have listed are great. With that amount of time I would suggest adding Vienna. Maybe be my favorite city over there.
I would do:
Berlin - 3 days
Prague 3 days
Vienna 2 days (or 3)
Munich 4 days (may include a trip to Neuschwanstein)
Lucerne 3 days (with a day trip to Fortress Furigen and Mount Pilatus area)

I wouldn't avoid anything in those cities. I've toured them all twice and loved them.

I would leave for this trip tomorrow!! Oktoberfest is my favorite place on earth. I think I may get to go back in 2015.

I also agree with touring Berlin, Prague and Munich in detail.

You could rent a car in Munich and head south toward Andechs (brewery), Neuschwanstein and into the Western Tyrolean region of Austria.
Go back east to Innsbruck and north to Salzburg and the Berchesgarten area--making a circle back into Munich.

The Austrian Alps is breathtaking scenery--just like Switzerland. And the region is so much easier and inexpensive to travel through than Switzerland. And you would scarcely be more than 100 miles from Munich at any time.

I love to drive northeast of Innsbruck to Zell-Am-See and south over the second highest mountains in Western Europe on the Grossglockner High Alpine Highway--ending up in Lienz, Austria. The south end of the Grossglockner is the most beautiful mountain scenery I've ever experienced. You can go through Cortinas, Italy (closeby) and catch the motorway/autobahn through the Brenner Pass into Innsbruck.