I've figured up that we've got 4.5 days excluding travel time to spend between Frankfurt and Munich before we move onward from there. Now, where to spend that and how long to stay on weekdays in mid-September traveling by train and/or bus?
Rhine Valley (1, 2 or 3 days)
Rothenburg ob der Tauber (0 or 1 day - actually an afternoon and overnight).
Munich (1/2 or 1.5 days) - We've seen Dachau on a previous trip in between trains but none of the city to speak of.
Neuchwanstein (0 or 1 days).
Rhine Valley: I'd spend at least 2 nights here. Bingen is probably the best logistically-sound option as it's at the beginning of the most scenic section and close to FRA (1 hour) and to Frankfurt (I assume you're coming from one of those) and also closer to your Bavarian destinations than the other options to the north. Stay at the NH Bingen? It's on the mile-long river promenade and steps from the KD boat dock for your river cruise. Views are awesome.
http://www.openstreetmap.org/way/162602472#map=18/49.97017/7.89197
http://www.nh-hotels.com/nh/hotel-gallery/fachadas-16415--nh-bingen_t2-z2w.jpg
http://fischerco.de/fc/upload/objekte/Palazzo/Rheinterrasse.jpg
You will want to cruise this part; Bingen - St. Goar takes 1.5 hours: http://www.bingen-ruedesheimer.com/images/map/rhine-valley290.jpg
Be sure to visit Bacharach, Oberwesel and its old town wall and St. Goar (Rheinfels Castle) which are all on the same river bank as Bingen (and easy to reach by train.)
From Bingen a passenger ferry gets you across to Rüdesheim all day long.
I'd strongly recommmend a train outing to Braubach as well - beautiful old-world town, Marksburg Castle (never-destroyed medieval castle.)
Braubach:
http://djtravel.homestead.com/files/braubach_-_hotel_1610.jpg
http://www.romantischer-rhein.de/uploads/pics/Altstadt_02.jpg
https://c1.staticflickr.com/5/4143/4751924826_36d7071291_b.jpg
About Bingen-Rothenburg-Munich... is it worth the stop in Rothenburg? Some considerations...
I'd spend 2-3 nights along the Rhine - we enjoyed Bacharach - then head straight to Munich for the remainder of your time.
As Russ says, Neuschwanstein is overrated. Although I'd still consider going. For me it is the setting and story rather than the tour of the castle that were intriguing. Nymphenburg is stunning but a different kind of experience. I'd say it really depends on how much time you have for Munich and how important it is to you to see Neuschwanstein.
We recently visited the areas you are going to and disagree with some of the other comments. We throughly enjoyed both Rothenburg and Neuschwanstein and didn't think that they were too touristy. Rothenburg is a unique town and in the beautiful Tauber valley setting. Neuschwanstein is also very interesting and if possible a visit to it should include a visit to nearby LInderhof. We thought that the Rhine valley was nice, but some what industrial. The Marksburg castle is an interesting castle and probably the best one to visit on the Rhine since it one of the few remaining middle ages preserved castles. On the whole, we preferred Rothenburg, Neuschwanstein and Linderhof over the Rhine valley and its sites.
I just re-read my post and realized I may have given the wrong impression. I do think Neuschwanstein is worth visiting but I personally don't think the tour is worth the money and possibly long wait. If you can fit a visit to Linderhof in, I would highly recommend it. For me it is the best of King Ludwig's 'castle' experiences.
