The following link will take you to a pdf for the Germany by bike guide. This is an excellent starting point and one I have used for several years.http://viewer.zmags.com/publication/16f ... 16f8a1ad/1
A few suggestions. You can link one of the prettiest bits of the Rhine Cycle Route to the Moselle Route. They join at Koblenz. The northen part of the Rhine Route is indeed fairly industrial but the Rhine Gorge from Koblenz to Mainz is lovely. The Moselle route is just gorgeous!
The Elbe route in it's southern reaches, around Dessau, is quite pretty and easy riding.
The Main, Tauber, Altmuhl route is another delight but can be a bit hilly in parts. It intersects the Romantische Srasse which is also very pretty and which, eventually, links to the Danube route.