Rothenberg ob der Tauber or Neuschwanstein area?

I have been to both and they are very different. Like which do you want for dinner, fish or chicken?

Just one word though, if medieval architecture is important you should know that Neuschwanstein is most definitely not that. It is a fantasy built to satisfy a whim at the end of the 19th century. It opened when Grover Cleveland was president of the US, 1886. One year before the Eiffel Tower started construction and 3 years before it opened in Paris.

We plan to end up in Munich for a couple of nights... We love beer, wine, medieval architecture, and beautiful scenery -- all of it!

Assuming 13 nights total and those 2 nights are numbers #12 and #13, and that you're flying out of MUC, maybe you should spend some of day #13 and night #13 in Freising instead of Munich proper. Freising probably fits your criteria better than Munich. And the Weihenstephaner Brewery is nearby. And Freising is much closer to MUC airport as well - like a direct 12-minute train ride vs. 40-45 minutes from Munich. IME, the closer I am to the airport when I wake up on departure day, the better.

But back to your question...

I really think you should consider adding your two days BEFORE making the long trip south to Munich (or anywhere beyond, as your destinations are already pretty strung out.) Right now, you have a 1-night stay (Cologne, Night #5) sandwiched between Bruges and your Burg Eltz visit + "Rhein" stay (not sure where that is.) The Day 5 train trip (not completely sure how you are traveling either?) from Bruges to Cologne is 3 hours, so I will assume arrival before noon in Cologne. But is it necessary to sleep in Cologne? What if instead, you stowed your bags at the station luggage facility and gave Cologne 5-6 hours of sightseeing? You could then collect your bags and catch a train at around 5 pm to the Burg Eltz / Mosel River area - where you could sandwich in a nice 3-night stay that is in better tune with your needs for scenery and old-world architecture. Cochem on the Mosel is a straightforward trip of less than 2 hours from Cologne (lv. Cologne 16:53, arrive Cochem 18:41?) and an excellent base town for the walk to Burg Eltz (Cochem > Moselkern station = 15 min. train ride) and the other Mosel towns.

Location map for Cologne and Cochem

Cochem attractions

River cruise from Cochem to Beilstein?

Train trip from Cochem via the Mosel Valley Railway and the Mosel Wine Railway to small wine towns like Reil and Burg and Traben-Trarbach.

Bernkastel is about 1 hour upstream from Cochem and has some incredible buildings as well.

Burg Eltz itself will require most of one day. Once you're done with the Mosel, you're well positioned for your Rhine visit; it's about 1.5 hours by train to St. Goar (Rheinfels Castle and good base town for cruising the Rhine / daytrips by train to Bacharach, Marksburg Castle, etc.) Because you'd have nearly 3 full days on the Rhine, you might subtract one night there, thus allowing 2 nights in Würzburg (a convenient stopover on the way to Munich.)

I struggled a bit to piece together your original plans and exact intentions, so feel free to clarify if I got it wrong. Here's my outline:

A'dam (2) - Bruges (2) - Cologne + Cochem/Eltz (3) - Rhine (2) - Würzburg (2) - Munich (1) - Freising (1)

I have never been to Munich but have been to both Rothenburg and Fussen. I was not a fan of Neuschwanstein but loved Fussen. I would do both of those instead of Munich.

I’d choose Rothenberg ob der Tauber. It’s nice after the day trippers leave. Wurzburg is nice. Ensure to walk to the Marienberg Fortress up on the hill. The Würzburg Residence was nice to visit too.

We do plan to have a car in Germany, to allow us some freedom to not be super scripted. We will likely explore the Mosel from Boppard, or after Eltz Castle, or both. I’m speaking with my uncle this weekend who has taken many trips to Germany and spent a good deal of time on the Rhine. Appreciate the tips! Thanks! We may spend more time on the Mosel, too. Undecided. You seem to be a big fan, Russ!

Yes, the lack of history in Neuschwanstein is what deters me from trekking so far. It’s an interesting history, no less. And a beautiful setting. Just curious if the surrounding area has enough to make it worth the trek. The trip to Rothenburg/Wurzberg could be realistic stops on the way to Munich from the Rhine, but Neuschwanstein is a whole other trip, and while I would LOVE to see the Alps, I think we may just need to plan a trip with that specific purpose, perhaps in another country, even, and not so much city-hopping.

The Wurzburg residenz palace sounds more interesting to me, and something a bit different than yet another castle. But again, it’s not perched lakeside on a mountaintop in the Alps :)

Is Zugspitze cable car as crowded as it seems in Rick’s guide video? It’s also not cheap.

I want to see the Cologne Cathedral lit at night (a childhood dream), and three hours on a train from Bruges feels like enough traveling for one day, so an overnight in Cologne made sense. We would like to see a bit of a city people live in (likely arriving in Cologne early afternoon, 1:00ish, obviously see the cathedral and likely rent a car here). Then the Rhine, then, more realistic to our route, Wurzberg/Rothenberg (of which I am still debating and seeking advice on), then Munich, then home.

Cala, what was such a draw to Fussen for you? Did you visit Garmisch-Partenkirchen, too? Why not Munich?
Our draw to Munich isn’t huge, but there’s some. We like the idea of the oompah band at Hofbrauhaus (I’ve been to local Oregon Oktoberfests with my German father, but my husband has not been graced with the fun). And my artist husband would possibly like to visit one of the art museums in Munich, if possible. Also, just seeing "normal" life, rather than just tourist spots, wouldn't be awful in our opinion.

I’ve been 3 times to fussen, will be making my fifth to Rothenburg this year. You can’t go wrong with either, but I would choose Rothenburg

Another vote for the magical town of Rothenburg!

"We will likely explore the Mosel from Boppard, or after Eltz Castle, or both."

I'm a fan of many parts of Germany, but with the priorities you have (wine, scenery, architecture) and the volume of those options on the Mosel River - and with the Mosel going completely unmentioned in your plans - I figured I'd better lay out the option for a stay there and allocate the extra time needed for it. Würzburg and Rothenburg, already in your sights, could still be visited with 2 nights there on my suggested plan. But neither offers the kind of experience you'll find on the Mosel.

With a Boppard base, you might be able to drive along some or most of the Mosel River route, but to actually explore and experience a few things, you will need a couple of full days on the river, without the round-trip commute from Boppard, and in addition to any Rhine sightseeing you have in mind. The curvy-windy Mosel road is no expressway - it usurps a lot of ground travel time and keeps you locked up in the car for too many hours. If you only want to pay a visit to Cochem, you could do that easily enough from Eltz or Boppard. But much of the Mosel's charm is upstream from Cochem, so for more, you should get yourselves a base in Cochem or some other place nearby for 2-3 nights in addition to your separate base in Boppard for your Rhine visit.

Note about wine: The car is a symbol of freedom but driving puts the vise-grips on spontaneous wine sessions. If you're serious about wine on the Rhine and the Mosel rivers, use the trains for your outings.

Some hotels in the region - and ALL hotels in Boppard - participate in the VRM Guest Ticket program, which offers spontaneous train travel at any hour to any of the towns within the VRM zone.

Went to Garmish and surrounding area in Oct 2019. We used Garmish as a base and hit Oberammergau, Neuschwanstein, Innsbruck, and other small towns in the area. It was great but you probably need a few days to explore. Even though it wasn't historic still enjoyed the castle.Garmish is surrounded by the Alps and central to these locations. Oberammergau will be busy this summer because the play is going on, which was postponed for 2 years. We are going to Rothenberg this summer for the first time on the way to river cruise from Nuremberg - heard it is a great stop. Good luck.

Rothenburg is an authentic medieval city, Neuschwanstein is a fake castle only about 200 years old. Both are still worth seeing. The Garmisch area has a lot more to see and do with going up the Zugspitze and some of the other sites in the area.

However, the Romantic Road (includes Rotheburg) has several medieval walled cities that are worthy of visiting.
https://www.romanticroadgermany.com

While I haven't been to Rothenburg (yet?) it's undoubtedly a wonderful place; however, based on your itinerary you're likely to visit a number of charming medieval towns and villages during your trip. On the other hand, Neuschwanstein is a spectacular one of a kind place in a beautiful setting! Couple your visit with Hohenschwangau Castle (it's within walking distance - visit here first). Plus, your friends back home will want to hear about your fairy tale castle visit and have probably never heard of Rothenburg. Don't make it a day trip from Munich but spend the night in the area. As your research has shown, there's a lot to do south of Munich in Bavaria. Another place we enjoyed was Wieskirche - a beautiful rococo church that's a quick stop. From Munich to Neuschwanstein via Wieskirche is only about 3-3.5 hours by car including your stay at the church. BTW - the Hofbräuhaus is fun with great beer and sausages and make sure to visit some beer gardens (Augustiner-Keller, Chinese Tower) in Munich as well. Also, your husband will enjoy the museum district (Kunstareal) - the Alte Pinakothek is grand and has one of the da Vinci paintings (Madonna mit der Nelke).

Thanks, everyone! We have decided, for the sake of not doing too long of a trip, to visit Würzburg on our way to Rothenberg ob der Tauber from the Rhine, then to Munich for 2 nights. I appreciate all of your thoughtful replies, and we have much to look forward to in another trip for exploring more!