3 weeks in Germany - need itinerary help!

Salzburg is a day trip from Munich for most people. Cologne is a rather ugly postwar city with one famous and several interesting churches. Rust is either out of the way or the Romantic Road is a detour from Rust to Munich/Salzburg. You spend 1/3 of your time in Southern Bavaria and 2/3 of your time in Southern Germany, with a big hole between Berlin and the rest of your stops.

I would skip Cologne and use Frankfurt or Mainz instead as a base to see the Rhine, add a stop between Berlin and Frankfurt/Mainz, skip Rust to streamline the itinerary and use a single base in Southern Bavaria. Something like this:

Berlin - 5 nights (day trip to Potsdam)
Quedlinburg/Harz mountains - 3 nights (day trips to Goslar, Wernigerode or steam train to Brocken)
Frankfurt - 3 nights (Rhine)
Romantic Road - 3 nights
Munich - 6 nights

In case you wonder about Quedlinburg: read the reviews
More streamlined, no holes, more balanced.
You could also exchange Quedlinburg with either Thuringia or Saxony, both between Berlin and Frankfurt. Rick Steves calls Thuringias capital Erfurt a untouristy Rothenburg, while Saxony offers, among other things, Saxon Switzerland, which are probably Germanys most picturesque mountains.

I agree with Martin that 5 nights is good for Berlin, if you have to reduce something else to get 5 nights there, then take 1 from Munich. That would still give you 7 nights in Salzburg-Munich area which is good.

I disagree with him about Cologne though, I didn't stay there so was only there for the better part of one day but I enjoyed it a lot. The cathedral is one of the most famous in the world (if you like that kind of thing you'll love it) and the Roman-Germanic museum was fantastic. I even enjoyed the 1 hour boat cruise on the river, even though it's not picturesque it's very interesting and informative. Lots of nice cafes in the old town area around the cathedral also. I went there mostly because the cathedral was on my 'bucket list' and it was worth it.

We recently visited many of the areas you plan to visit. Looks like a good plan, here are my comments:
Consider visiting Riquewhir or Colmar France when you are in the Black Forest area - very beautiful areas of Alsace France.
Visit Rothenburg on the Romantic Road - even though it can be crowded with tourists, it is very interesting and well deserved reputation as a preserved Middle Ages town with a lot of sights to see.
Salzburg is a great, compact city to visit. 3-4 days if you include Berchtesgarden
I think that 5 days is too long for Munich. Also you should visit near by Neuschwanstein, Linderhof and their near by towns.
Are you driving or taking public transportation? Each has advantages and disadvantages, but traveling by car gives you more flexibility in visiting smaller towns and the countryside.

Instead of Cologne, I'd stay in Boppard or Bacharach and see sights around there. I'd use Rothenburg as a base for the Romantic Road stretch. Am not familiar with Rust, but 2 nights in either Baden-Baden or Staufen would be well spent. The rest looks about right to me. Have fun.

Here are some suggestions for 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.

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 would add more nights to Salzburg. 3 nights/2 full days isn't enough time if you want to see more than Salzburg. Maybe take one or two nights from Munich.

Salzburg
Berchtesgaden
Konigssee (and Jennerbahn cable car) by Berchtesgaden
Eagle's Nest by Berchtesgaden
Salt Mines Berchtesgaden
Rossfeld Panorama Road above Berchtesgaden (if driving)
Salzkammergut / Wolfgangsee
Hallstatt
Hallein, Austria (Salt Mines)
Werfen (Ice Caves and Hohenwerfen Fortress)
Right between Munich and Salzburg is "Mad" King Ludwig's Herrenchiemsee Palace

Just some ideas.

Paul

Thanks so much everyone for your responses! We will be changing up the itinerary to skip Cologne as it doesn't seem to be the strongest part of our itinerary, and because it is quite out of the way, so we'll be adding in some of the stops that you recommend :)

Martin - Quedlinburg and the nearby areas you mentioned look really cool! Thanks, we'll definitely consider stopping there.

Nancy - good to know, we'll definitely be adding a day to Berlin so that we can spend 5 nights there. And thanks, we will have to see Cologne on another trip - the cathedral does look fantastic! But it seems like it's quite out of our way for this trip. But we'll be back! :)

hamiltonpa - Awesome! I'm glad you had a fun similar trip :) We'll see if we can visit France while we're there, that would be really cool. We definitely plan to visit Rothenburg while we're nearby, it looks pretty amazing. The 5 days in Munich would include some day trips including Neuschwanstein, Linderhof, etc - would you still say 5 days is too much time there? And we'll be taking public transportation everywhere I think. We may rent a car in Nuremberg/Romantic Road area to have more flexibility with local day trips.

Prof B - Boppard and Bacharach look great! They may have to wait till next time we visit since we might be traveling more down East Germany now since we're trying to simplify the itinerary a bit. Rothenburg looks so pretty, I definitely have to see it and we'll consider spending some nights there. Baden-Baden & Staufen look great as well, I'll try to see those areas too.

Jeff - Wow, what great ideas here. I will definitely have to see as much as I can, a lot to look into here. Thanks so much!

Paul - Salzburg does look wonderful, I'll consider adding more days there! Thanks for those suggestions, we definitely want to see Berchtesgaden & salt mines and I'll have to research the rest - that all sounds really amazing.

Graynan8502 - great! Glad to hear we won't need a car in Berlin, we are planning on using public transport for most/all of the trip. I think we're getting in on a Sunday morning, so hopefully we'll be able to visit the flea markets since that sounds like fun and the Sputnik theater looks great as well. Since we'll be flying back from Munich we'd need to change up that itinerary a bit, but the routeperfect website looks so helpful for planning!

Thanks so much everyone, I feel a lot better about planning this trip and I'm really looking forward to going! :)

Hi MrsEB, thanks! I didn't list Frankfurt on the itinerary, so I'm not sure where you saw that. But one commenter suggested that we might stop there to see the Rhine. Still, since several have not recommended Frankfurt, we had decided to skip it.

But our current/revised itinerary is something like:
Berlin - 5 nights
Dresden - 2 nights
Nuremberg- 4 nights
Rust - 2 nights
Salzburg - 3 nights
Munich - 4 nights

"Rick Steves calls Thuringia[']s capital Erfurt a[n] untouristy Rothenburg"

Well, they both have a lot of red-roofed buildings. Other than that ....

Erfurt is about 200,000 population vs 10,000 for Rothenburg. Is there a town wall in Erfurt; I couldn't find it on Google Maps.