Germany 14 Day Itinerary

5 nights In Rhine valley/Mosel Valley (should we split our nights in
each area?)

You might look for one place to stay in Braubach for all five days. From there you could easily get to both the Mosel (change trains in Koblenz) and the Rhein, plus you could visit the Marksburg, which is in (above) Braubach.

You do not mention if you plan to travel by train or car, which would make splitting your nights in the Rhine/Mosel easy by car, but more difficult by train. A car would be headache in the cities, of course, but would give you far easier access to the charming villages of Bavaria from Munich. Personally, I prefer to sleep where I am sightseeing, spending less time on daily travel, but some people prefer a central location and day trips. You likely know your own tastes there.

Granted Oktoberfest is touristy, but if you are a student of German culture there is no substitute for experiencing it yourself. If you have no particular interest, it may not be worthwhile to you. I would assume it will boost hotel prices in Munich substantially. An alternative is to stay on the perimeter with S-bahn access to the city and a car to explore Bavaria and perhaps Salzburg. A car would also allow you to spend time in Alsace from the Rhine valley, which is a splendid use of a day.

Enjoy your planning, you will have a wonderful time.

Where are you flying from and back to? If the US you might have better direct flight options to, or from Frankfurt, putting the Rhine/Mosel at one end of the itinerary rather than the middle.

Oktoberfest is a genuine cultural event full of locals. Not going would be like being in New Orleans and skipping Mardi Gras in the French Quarter because tourists go there.

Thank you for your replies.
We plan on using only public transportation for the trip.

Stan - we are flying from the NYC area so luckily there are direct flights for us to Berlin, Munich and Frankfurt.

Consider reversing your itinerary such that you are on the Rhine on Sept. 16. There's a wine festival in St. Goar over that weekend with the "Rhine in Flames" fireworks exhibition Sat. night. I believe neighboring Oberwesel and St. Goarshausen across the river will be participating that weekend as well. These very small towns (and their neighbors) book up well in advance for wine fest weekends. If you schedule a flight out of FRA that's not too early, you can sleep in one of the Rhine towns the night before and catch a train into FRA from there. The Rhine fests are very civilized events - not inebriation marathons - where you really do get an eye on local culture and lifestyle and mingle with not only, but mostly, German locals and visitors.

I could see 2-3 nights in a Mosel town like Cochem and 2-3 nights in a Rhine town. (I do not see any difficulty moving from a Mosel town to a Rhine town by train.) I like Braubach but if splitting your stay, for strategic reasons I would probably choose St. Goar instead (which has a ferry that shuttles you across all day long, making a train ride or a drive to Braubach / Marksburg Castle easier.) Of course in St. Goar you won't have to return to some other base after the Saturday night fest. Note that staying on the Rhine for both Rhine and Mosel is OK if you plan to travel up the Mosel to Cochem, but it makes for a fairly long day outing if Bernkastel or Trier is in your itinerary.

There are some good ways to get "off the beaten path" in Bavaria but you probably won't accomplish that from a Munich base. You might consider 2-3 days in Franconia prior to or after your arrival in Munich (and spend 2-3 days there in the city.)

Some photos of places in Franconia and other parts of Bavaria that most foreign tourists don't venture:
Iphofen: http://www.stadtbild-deutschland.org/forum/index.php?thread/2985-iphofen/
Marktbreit: https://upload.wikimedia.org/wikipedia/commons/3/3e/Marktbreit_BW_6.JPG
Pappenheim: http://www.frankentourismus.de/timm_images/orte/30/pappenheim.jpg

BTW, the only place I've mentioned that lacks train service is Bernkastel (but there are frequent buses to Wittlich station on the main Mosel train line.)

Germany is filled with great regional harvest fests in September, most of which the international frat boy and woo-girl demographics have yet to discover (and subsequently ruin). If you want a similar without the bro-dudes, look into Stuttgart's Canstatter Volksfest, Bad Durkheim's Wurstmarkt, or any number of other regional fests.

Thanks everyone for the advice! Over the next few weeks we'll be working on the itinerary.