Hi gfibbs,
My second RS tour was Berlin Prague Vienna which was wonderful! Berlin has been on my list of places to make a return visit.
I'm going on the Munich Salzburg Vienna tour in December which will not include Berlin, obviously. But next year, my sights are set on the Best of Germany tour and will likely sign up in a few weeks (work issues) which will take me back to Berlin.
With that as context, I would suggest the Best of Germany tour for the overall experience of history, culture and art. My friend and I are especially interested in the history of Martin Luther, the Rhine River area and Rothenburg too. It begins in Hamburg where I have wanted to go also.
Bottom line is, I don't think you can go wrong with either tour. If you want to see it all, the Best of Germany tour is the one I think. It will give you an excellent overview of the entire country.