Germany two week itinerary help

I can't speak to the Bavaria section of your trip. But for Saxony and Berlin, the train is very easy. You can use a Saxon Ticket for your daytrips from Dresden to Leipzig and Goerlitz. And for Goerlitz, there are only local trains anyway, so the Saxon Ticket is the most sensible way to go. From Berlin to Potsdam, you take the local S-Bahn. From Dresden to Berlin, you can book advance tickets at a discount. When we did this in September 2012, it was €38 per person if bought at the last minute, but €19 for one person and €29 for two people traveling together if bought in advance (so we saved €47, each way). You book at http://reiseauskunft.bahn.de/bin/query.exe/en, print out the PDF (even though it says to use A4 paper, 8.5 x 11 is fine) and show your credit card with the printout to the conductor. They scan your printout, swipe your card, and you're set. For this route, a Helpline contributor recommended reservations, and I'm very glad we got them. For €4 each, we had designated seats together, which was very handy because the train was quite full (people were sitting in the aisles on their luggage). But we just went to our reserved seats, stowed our luggage, and settled in. If you can commit to specific days of travel (and it sounds like you have a definite itinerary in mind, rather than meandering around), similar discounts should be available for your other non-regional train segments. With these discounts, it's going to be hard for a car to be cheaper.

Speaking to the Bavarian part of the question. Parking in and around Munich can be a bit difficult but it can be done. More difficult, I would have thought, for as many as 4 nights. Dachau can be done either by bus and train - very easy -, or by car. I've done it by car and parking was very easy. If you do have a car, Andechs monastery has good food some distance southwest of Munich, and I have heard that their beer is acceptable, too. Neuschwanstein is easy by train and bus, and easy by car too although the car parks near the "castle (you know it was built in the 19th century?)" are expansive. The Sommerrodelbahn is easier on your own wheels. It doesn't operate if there is a hint of rain in the air or heavy dew. There are others around too, generally easier with a car. Nuremberg is very easy by train from Munich and the town is very easy to get around. The autobahn between the two works pretty well too. On one trip we stayed at a chain hotel with included parking in the suburbs and took the U-Bahn in. On balance, train is easier. Getting to the Eagles Nest is a wash, too. Easy either way, although it is very convenient to Salzburg by car. If you want to drive to Salzburg and stay just out of town with free parking, easy bus to centre, and very good food at a good price I know the place. Traffic in and around Munich has frequent stau.

Thanks for your thoughts so far. To be clearer, i wasn't thinking of renting a car for the time period we are in Munich or Berlin. It would be pick up in Munich on our last day and off Berlin as soon as we get there.
That said, if we did rent a car, is there a relatively easy way to go from the castles to Eagles nest? Is staying in Salzburg inevitable? (We are not that interested in spending time in salzburg.)can we get away with only one overnight down south and then get moving north after seeing eagles nest? Or, should i just try to pursuade my husband that eagles nest isn't worth the extra time ;) ?

"Eagles Nest" worth it or not not worth it? That is for the two of you to decide. What made you consider going originally? Is either of you a history buff? WWII interest? Interested in where a man in a funny mustache did things? Want to see a stone fireplace with marks made by occupying USA troops? Yes? Go. No? Don't go. Don't go just to see a mountaintop - there are hundreds all around and more on your route. No, you don't need to stop in Salzburg if you don't want to.