Ideas for Germany itinerary

Copying my post in a recent thread about day trips from Munich without throngs of tourists:

My favorite is to take the S8 southwestbound to the end of the line at Herrsching. Walk a couple hundred meters to the lakefront and board one of the stately paddlewheel ships which cross the Ammersee to my favorite untouristed Bavarian village, Dießen am Ammersee. Dießen is a popular destination for German weekenders, but it's not on the international tourist grid at all. Walk through Dießen up to the baroque-rococo Marienmünster Abbey (1730). Return to Herrsching by ship and take a taxi or bus, or walk three miles up a forested trail, to Kloster Andechs, where Benedictine monks have been brewing great beer since the 15th Century. (Photos of Herrsching, Dießen and Andechs here)

Or take S2 about 20 minutes from Hauptbahnhof to Oberschleißheim, and visit the magnificent, colorful Schleißheim Palaces, summer home of the Bavarian royal family. Aviation history buffs will enjoy Flugwerft Schleißheim (aviation branch of the Deutsches Museum), a short walk from the Schleißheim Palaces.

If you have a free Sunday, go to the spa town of Bad Wörishofen, birthplace of naturopathy. Therme Bad Wörishofen is a wonderful spa/sauna/waterpark complex. Then go to the open-air cafe on the small grass-runway airfield on the north side of town and watch skydivers do their thing, while you wait for your 45-minute ride in a classic 11-seat, Soviet-built Antonov An-2 biplane (advance reservation required; photos here).

Tourists have yet to discover Ingolstadt, a charming, friendly town about halfway between Munich and Nürnberg. There are many historic buildings in the old center, including the former Anatomy Building of the University of Ingolstadt, now the German Museum of Medical History. Gardens in the courtyard are made up of medicinal herbs and plants. The building was the setting for Mary Shelley's original 1818 novel Frankenstein. Tours are available of the Audi factory, just outside the old center. Ingolstadt self-guided walking tour available here.

In Munich itself, the self-guided walking tour in Rick's Germany guidebook is excellent. It can take anywhere from two hours to two days, depending on your level of interest and curiosity.

For insight into Munich's dramatic role in the rise and fall of the Third Reich, visit the new NS Doku-Zentrum, which just opened last May. It's on Briennerstraße, on the site of the Third-Reich-era Nazi headquarters building. Führerbau (Hitler's office building, where the 1938 Munich Accord was signed) is next door, repurposed as a High School for Music and Theater. Historic Königsplatz is across the street. The City's website offers free downloadable maps and audioguides for self-guided walks tracing the history of National Socialism in Munich.

I've been to the Black Forest a couple of times, and it was okay. If your time is short, it might be better spent elsewhere.
We have enjoyed the Rhine River Valley--from Cologne south to Koblenz and Bacharach. The Duomo in Cologne is absolutely incredible, and the city has more nightlife than they're given credit for.
We're also fond of Munich as a 4 day destination and running 2 hours east to Salzburg. We also like dropping south into Tirol and the Austrian Alps. It's hard to beat a good Saturday night at the Andechs Brewery or other great beer halls in the region.
I've found that Bavaria Ben has great reviews on bed and breakfasts and other travel subjects on:
http://www.bensbauernhof.com

I'd go with option #2 or something like it - If you're spending some good time on the Rhine/Mosel, I don't think you'd gain that much by doing the Black Forest as well, and it would take up a lot of ground travel time.

Rhine/Mosel: 4 days, 4 nights (Use Boppard as a base town for all 4 or split your stay.)
Northern Bavaria ("Franconia") : 4 days, 5 nights (Bamberg probably is not the best base town for several reasons)
Munich: Visit on a day trip from Franconia (easy from Nuremberg.)

"Transportation advantages?"
I would probably stay 3-4 nights in Nuremberg (great for outings by train) and then 1-2 nights in Würzburg (mostly to shorten the trip to FRA for your flight out.)

Day passes for outings from Boppard:
http://www.vrminfo.de/en/tickets-and-fares/ticket-offers/leisure-ticket/
http://www.vrminfo.de/en/tickets-and-fares/ticket-offers/rheinland-pfalz-ticket/ (more €, covers more territory)

Day passes for outings from Nuremberg:
http://www.vgn.de/en/dayticket?&Edition=en&p=tagesticket-plus
http://www.munich-touristinfo.de/Bavaria-Ticket.htm (more €, covers more territory)

Thank you all for the fantastic advice, tips, and ideas! Do you see mid April being as good as late September, or early October? I don't mind a little fog. Makes for some neat pictures.

We have been going to Germany in April for the last few years. It turns out that April is on the average a dry month in many parts of Germany and we have had mostly sunny weather. We have of had some rain and even a touch of snow one year. The trick is to pack layers of clothes. You can always buy a cheap umbrella there if this becomes the rare rainy April. We are returning this April ourselves.

April is especially quiet along the Rhine River. Boppard will have rooms but some small towns might have a limited number of restaurants open. I have not been there at this time in years; so, it might have changed. We typically visit northern Bavaria and the area west of Munich, and everything is open. Munich itself is a thriving, always active metropolis.

Bamberg in April
https://mcchelsea.smugmug.com/Other-2/Bamburg-2014/

Würzburg in April
https://mcchelsea.smugmug.com/Travel/Empty/

Freiburg is a beautiful university town and a great base for exploring the Black Forest--day trips to Strasbourg and Colmar in nearby Alsace are easy and charming. I'd skip Basel (Bâle) just over the Swiss border unless you're particularly interested in one of the museums or other sights there. A day trip into the Black Forest could include some of the pretty churches/little towns (St. Peter) or lakes (Titisee).

Freiburg is the sunniest corner of Germany, but the weather in April is generally a little more iffy than September/October. One other thing to keep in mind is that it's a wine region, so the fall harvest season, with local festivals and pretty nearby wine villages like Stauffen, add to that region's charm.

Gute Reise!