Germany

It's unclear whether your two weeks include only Germany time or your time in Paris and Venice as well, and whether you want to spend anything but "go-through" time in Austria or Switzerland. It's also unclear if you've decided on driving or taking trains. What to see? Depends on your interests. Your Rothenburg and Neuschwanstein will mean quality time with tons of international tourists. You might want to linger in the Mosel Valley (Eltz) and Rhine Valley a while and visit some popular but less touristy places that will put you in touch with historical Europe and old-world Germany. Trier is Germany's oldest city with Roman ruins and history, if that interests you. Cochem, Bernkastel, Bacharach, Linz am Rhein, and Boppard are handsome villages near Burg Eltz with old-world charm that rivals Rothenburg; in these half-timbered, scenically-situated towns, tourism shares the stage with agriculture and the wine industry, while Rothenburg and Füssen exist for tourism only. And since castles interest you, you'll be surrounded by dozens of them along the Rhine/Mosel that are 800-1,000 years old; you can explore 800-year-old Rheinfels Castle in St. Goar as long as you like, but at Neuschwanstein (which is less than 150 years old and isn't a castle at all, just a mock-up of sorts) you are herded through in 30 minutes. Near Rothenburg, Nuremberg and Bamberg are handsome, interesting cities full of history that are worth considering as well.

Switzerland is a signficant detour on the trip between Füssen and Venice. I suggest you get your Alpine thrills in Bavaria and Austria.

Two weeks from Paris departure to Venice arrival? 1. Train to Boppard, 3 nights, see Burg Elz, Rhein castles, Koblenz, Mosel valley. Get a VRM minigroup 3 day pass to travel in the area. 2. Leave on 9 am K-D boat to Bingen for Rhine cruise. Proceed to Rothenburg by train. 3. 2 nights in Rothenburg so you get one morning and one full evening after the tour bus groups have left town. 4 Train to Munich. 4-5 nights to see town. Travel to Fussen and other day trips using Bayern ticket. 5. Train to Salzburg. 2-3 nights. 6. Train/Bus to Venice.
Skip Switzerland. Out of the way and overpriced IMHO.

I like Sam's itinerary. You didn't say if you will have a car or are planning on taking the train

Munich is a great city, I happen to like Cologne (and maybe Aachen) on this route a little better. Koblenz is a good base for daytrips, but not nearly as important a destination as Cologne or Rothenburg (for example). Although it's convenient to walk from (multiple) train stations to your hotel, we found upscale (I mean not-dated-or-dowdy, not seeking Four Seasons!) Koblenz hotel choices lacking in 2011. Like any big country, you should understand that you are not seeing "all" of Germany, whatever options you . You may wish to see other sections of Germany on a future trip. BTW, your mode of travel from Paris is a major factor in the route. Are you taking Eurostar via Brussels and then to the Rhine? That would point towards Cologne instead of Koblenz. (I concede that the scenic Rhine is not beside Cologne.) If you are flying anyway, why not see other parts of Italy on the way to Venice?