Frankfurt/Rothenburg/Munich in 10 days

"We hope to visit some of the Romantic Road via Rothenburg then onto Munich...Visit medieval villages and castles including Neuschwanstein....See the contrasts of German life, history, culture, sights..."

From the sounds of it, you'll have 4 nights together in Bavaria, then 1 night together in the Frankfurt area, then 4 nights independently there - do I have that right? You are going to have to be choosy about how you spend your time, given those goals.

If you're interested in real German history and culture, be careful that you don't get hypnotized by the "shiny objects" in the travel brochures! N'stein and Rothenburg are "red flag" destinations. N'stein isn't a genuine castle, and certainly not a medieval castle. Work was completed on it about 120 years ago. It was conceived by a theatrical set designer and lived in for a mere 6 months by Bavarian King Ludwig. It will cost you almost a full day to make a day trip there from Munich - but the tour lasts just 30 minutes! Rothenburg (which Rick Steves admits resembles a "medieval theme park") was "real" enough before it was heavily damaged in WW II but what you find there today after the rebuild is an intense level of tourism - in fact, the town's only genuine enterprise today involves feeding, housing, and entertaining 2.5 million tourists per year (and selling them lots of stuff, of course.) And of course English is spoken everywhere because of all the visitors, probably as much as German is, so I don't think you get a whole lot of authentic culture here. Still, it's worth a few hours if you're in the area... and this is a really nice area. Look into these places if you want a better picture of German life, culture, history, places that live and breathe German history and culture, and where there are not so darned many international tourists:
Würzburg
Würzburg's Residence (UNESCO World Heritage)
Nuremberg Old town
Nuremberg sights
Bamberg (UNESCO WH) - "Bamberg is an outstanding and representative example of an early medieval town in central Europe, both in its plan and its surviving ecclesiastical and secular buildings."
If you really want some history and culture, take a peek at how they lived in this area 400, 500, 600 years ago at the excellent Freilandmuseum in Bad Windsheim

I would spend those first 4 nights all in a Würzburg hotel near the station (which is only 1.5 hours from FRA.) Würzburg is an excellent train hub. I would day trip by train from there to Nuremberg and Bamberg, and possibly to Bad Windsheim and Rothenburg. I would buy a normal ticket from FRA to Würzburg and back to the Frankfurt area. I'd do these day trips on a Bayern ticket day pass (€28 for two adults per day.) And I would forget about Munich and anything else to the south if you have to get back to Frankfurt on that 5th day.
"Visit Rhine Valley... "
If you want to see a castle together when you return to the Frankfurt area, go to Marksburg Castle in Braubach, on the Rhine south of Koblenz. Marksburg is the real deal. Visitor information is HERE. Braubach is a delightul old world town - maybe stay there.

It sounds as if you need to research the area a little better in travel guides. I suggest Rick Steves' Germany, especially since he put Rothenburg ob der Tauber on the travel map.
The train to Rothenburg is about 3 hours, and takes a couple of transfers.
Bavaria Ben's new revised website at http://www.bensbauernhof.com has great information on this region.
If you're interested in traveling down the Rhine, I'd suggest going as far as Cologne to see the Duomo. We've stayed a couple of times in Bacharach in some great B&B's.

Yes, the German Rail Pass is sold there at Frankfurt airport train station. The Twin discount gives you a better price for traveling together, but note that when you split up, only one of you can take the pass and use it. Separate passes for a single adult and a single youth cost more.

Or, since it's not hard to stick to regional trains during your smaller-town connections, you can use the cheap, region-specific Lander Tickets on a few days, plus an advance-discount ticket for the one longer ride from Munich back to Frankfurt. See http://www.ricksteves.com/travel-tips/transportation/trains/germany-rail-passes#ticket-tips.

If you want a medieval village, head to Büdingen and Gelnhausen. Only an hour from Frankfurt, a group day ticket will set you back 27 euro. Total. The church in Gelnhausen is magnificent and it was built early 1200's. Neither of these towns were bombed in the war.

Favorite town on the Rhine is Eltville, lovely promenade along the river, with no roads or train tracks in your way. Lots of half-timbered houses, wine bars, and one of the older Monasteries is near by. Eberbach, just a short bus ride from Eltville.
A Hessen ticket for 33 euro will be good for the day for both of you.

Other medieval towns - Limburg, Marburg, Idstein, or Seligenstadt. All within one hour of Frankfurt with cheap train tickets for the day. Use www.rmv.de to find trains and prices. None of these towns were bombed.

I am traveling with a 12 year old daughter, flying in/out of Frankfurt. I have 5 days with her. Should I hub out of Frankfurt or another city? What are the best spots to visit, see, do?

"Should I hub out of Frankfurt or another city? What are the best spots to visit, see, do?"

Well, you have some good options.

Your first plan (Bavaria - medieval - castles - Rhine, but mostly in Bavaria) makes the Würzburg-based option (with a separate trip to Marksburg) suggested above a reasonable one.

But if you don't have to be in Bavaria, the Rhine/Mosel region is an equally desirable choice for 5 nights. There are 40 genuine castles in 40 miles of river valley. There are numerous towns with half-timbered buildings and old town walls and towers. There's an open-air museum (like the one in Bad Windsheim) that showcases rural life over the last 5 centuries. There are WW II museums, There's a lot of "fun stuff" too in the area - free-flight falconry exhibitions, chairlift rides, summer bobsled runs, river cruises. And a visit to either Cologne or Mainz would provide the "contrast" you first mentioned. Transportation in this area is especially good and inexpensive as well. You won't need a rail pass.

(Then when you have those days to yourself, you could visit Frankfurt, Büdingen and Gelnhausen, as Jo suggests, or maybe the Würzburg area.)

I would look for a room or an apartment ("holiday flat") in Bacharach, Oberwesel, St. Goar or Boppard, all on the west (left) bank of the Rhine, for the greatest ease of getting around. Book 4 nights, with a 5th night in Mainz (near Frankfurt.) St. Goar enjoys the most scenic natural setting; Rheinfels Castle is right in town, and there's a ferry crossing for convenient access to trains on the other river bank (important for getting to Marksburg Castle and the summer bobsled if that sounds fun) so I'd check there first.

St. Goar accommodations
Rheinfels Castle
Summer bobsled
Boppard old town scene
Boppard chair lift
Oberwesel
Oberwesel old town wall
Oberwesel wine fest
Rhine Cruises
Open air museum Bad Sobernheim
Cochem (Mosel River)
Cochem, falconry show
Remagen WW II museum
Mainz, old town
Bacharach
Boppard chairlift