"Plan on renting a car at Frankfurt airport for duration of the trip as we like to take the less traveled roads and see rural sights."
I think a lot of us dream of traveling "the road not taken." Of course this is quite possible - but when the inevitable doubts about actually carrying out such a plan set in, many travelers summarily kick Robert Frost to the curb and pencil in a bunch of Rick Steves-approved destinations and accommodations instead (which I imagine is what you have done.) Like Rick's suggestions, your itinerary hits some of the Europe's most overrun places. Rothenburg and Füssen are notoriously overtouristed, and who has never heard of Vienna, or Salzburg?
The less traveled roads - and the lesser-known towns that you can also reach by train (and these are VERY numerous) really can be enjoyable. You just need to free yourself from the blue and yellow guidebook.
Ever heard of the Odenwald, Reichelsheim, Simonswald or Fußbach? Not that you have to go there. But if you wish to avoid sharing the roads and the towns you visit with the international tourist crowd, spend a little time reviewing some of the trip reports at Bavaria Ben's website. Ben and his followers have put together some enlightening pages that highlight both well-known and lesser-known destinations in southern Germany and Austria (and Switzerland too.)
Ben's 2012 trip
Trip reports from 1998 on
I generally agree with Lee that the train is no barrier to an itinerary based on rural towns. Like Lee, I prefer smaller places ; I have traveled in Germany for many years by car and by train and now use the train (and an occasional bus) exclusively. Trains are less expensive than car travel as well if you are armed with the proper information.