3 weeks Germany itinerary. Please critique

day 6 - (explore Schloss Moritzburg/Bastei/Rakotzbrücke/Leipzig/Karlsbad) -to be decided

Rakotzbrücke is a building site right now. And it's difficult to get there anyway (by public transport). BTW: the highlight of this town is Muskau Park, a World Heritage Site. If you are looking for a beautiful park with photo ops nearby consider Pillnitz Castle, on the outskirts of Dresden, instead. You can take the paddle steamer to get there.
Karlsbad is too far away for a day trip.
Leipzig is a interesting day trip, but the centre doesn't have real highlights, and the buildings are mostly from the 19th century. Not exactly what you are looking for.
Moritzburg can be done in combination with Radebeul, a town which offers a wine village (Altkötzschenbroda), several castles (among them Wackerbarth, Saxonys state winery), vineyards, a steam train (to Moritzburg), and a museum dedicated to the most popular German author of the 19th century, who mainly wrote adventure stories about the American frontier.
Bastei is a very nice day trip, but it can be crowded.

But since you wrote that you "love quaint little lanes that lead to a local coffee shop kind of beauty, while we also enjoy things of historical importance":
also consider Görlitz and Meissen, two beautiful preserved towns. Görlitz is actually Germanys best preserved town, with more than 4.000 listed buildings. It's a divided town after the Polish border was moved to the west in 1945, and today Görlitz preserves the heritage of German Silesia, a culture that died out with the expulsions after 1945. You can try Silesian food there, or visit the (very good) Silesian Museum in one of Germanys oldest Renaissance buildings.
Meissen is the cradle of Saxony and looks and feels like Pragues Lesser Town in small. A cute historic old town overlooked by a massive castle with a beautiful Gothic cathedral. And you can visit the porcelain manufactory.

Sounds in general like a good plan to me.

When is planned date of travel?

I like the mix of regions (even some are missing - no critique). With that you will get a mixed impression of local cultures in Germany.

With day trips I guess you are aware of double ways / more time for transport.

3 full days Berlin is ok, with maybe a visit of Potsdam palaces I would add a day.

Transport can be best done by trains.

I would suggest doing a day trip to Meißen, as suggested above, from Dresden...well worth it, culturally and historically. I have been there twice on day trips, still wasn't enough to enjoy and absorb the place.

Reduce the time for Rothenburg odTauber for spending it in Meißen or Görlitz...not even in the same league.

Thank you so much Martin, Markk and Fred for your insights. I've updated the itinerary as per your inputs.

Another few query:

1. Where should I stay for the Middle Rhine valley cruise/tour. Should it be Bacharach or Mainz? What would be convenient?

2. Also, for day 17 and 18, I'm not sure how to plan those days. Any tips?

Q1: Mainz is a very nice town. My favorite from living on the other side of Rhein is Eltiville. As you mentioned monuments also Rüdesheim can be an option with famous Niederwald-Denkmal. Drive by train - see link in my first post.

Q2: Normally tourists do a boat tour (example). Typical end point in south end are Rüdesheim (north side of river) and Bingen (south side oof river).

Thank you, everyone. Based on your feedback, I've almost finalized the itinerary. I've two doubts:

1. Should I get the German Rail Twin Pass Flexi - 15 days for EUR 750 which will cover all rail travel & have peace of mind. Or book Spartickets for the longer rides + regular day tickets for day trips within the region? (I did some math & the difference isn't that much)

2. If I should get the Rail Pass, it says it'll be delivered by postal mail. Am I understanding it correctly, Germany to my country delivered by post? Is there no online print option?

day 1 - fly to Berlin, rest, relax, get over jetlag, explore nearby places
day 2 - explore Berlin
day 3 - day trip to explore Potsdam palaces
day 4 -
day 5 - Berlin to Dresden, explore
day 6 - (explore Schloss Moritzburg/Bastei/Görlitz/Meissen) -to be decided
day 7 - Dresden to Nuremberg, stopover at Bamberg
day 8 - explore Nuremberg
day 9 - day trip to Rothenburg
day 10 - day trip to Regensburg
day 11 - Nuremberg to Munich, explore
day 12 - day trip to Füssen (visit Neuschwanstein)
day 13 - explore Munich
day 14 - day trip to Mittenwald
day 15 - Munich to Heidelberg, explore
day 16 - day trip to Black Forest
day 17 - Heidelberg to St. Goar (to Bigen & then K-D line ferry to St Goar) (Explore Bacharach, Oberwesel, walk to Rheinfels castle)
day 18 - Explore + Rhine valley cruise
day 19 - To Frankfurt, spend the night
day 20 - Fly out

Q1 is a mix of calculation and convenience. Guess that you can answer that only n your own.

Q2: on the booking page there is a link offerered for printable ticket ("If you'd like to have consecutive days and a ticket for self-printing, ...").

If you decide to go to Rüdesheim am Rhein, I would assume the Niederwalddenkmal is all refurbished, cleaned up, etc so that you'll get a great view of it. When I was there last a few years ago, it was all covered up, obviously, being refurbished, etc. You couldn't see anything, hadn't seen that since the first time in 1977.

Just as interesting then was the train station (if you can call it that) in Rüdesheim where photo posters along the wall relating to the war and German soldiers and the aftermath could still be seen, all written in German...poignant and revealing.

I saw likewise in Sigmaringen (train station) in 1971. The small towns still had these affixed along the walls.

The Niederwalddenkmal was bright and spiffy in September 2018.

Thanks,,,fantastic !

In 1977 the Denkmal was black which I was used to seeing but it did have some graffiti on it, which was surprising. I took slides of that monument.

Pretty good plan.

One suggestion, Don't do a day trip from Nuremburg to Rothenburg on the Tauber, just go there and then head on down the Romantic Road. Visit Dinkelsbuhl and Donauwurth and possibly Augsburg before arriving in Munich.

I am not clear why day 4 remains blank. In my opinion, you need at least another day in Berlin. The Museum Island, alone, will consume more than a day. I’m not sure, but I think you can reserve tickets for the Pergamon Museum.
The Reichstag is an absolute must-see. Reserve a tour in advance. I believe it’s the only way to see the interior.

There is a castle to be visited, Scloss Charlottenburg. If you go, there are two small museums a few steps away. The Berggruen Collection houses a large number of modern works, think Picasso, Klee, Giacometti, Braque, etc. the Brohan Museum showcases Art Nouveau and Art Deco works.
Then there are Jewish sites. The Jewish Museum is notable not just for its content, but for its architecture, as well. The Memorial to the Murdered Jews of Europe doesn’t take long to see, but should be experienced.

A German Rail Twin Pass is a good idea but you do NOT need 15 days.

The smartest way to use a German Rail Pass is for long-distance trips using the ICE (inter-city express, i.e. the "fast") trains. Because those are the most expensive journeys.

Sometimes it's not the worst to use a rail pass day for shorter distances where it's still most practical to use the ICE or an IC.

It is a total waste of money to use the Rail Pass on days that do not involve travel on those class of trains, however. You can always get local day tickets that will be cheaper than using a Rail Pass day.

Without plugging in the trail routes I see 6 obvious Rail Pass days on your original itinerary. I'd have to get into the weeds regarding day trips to Fuessen or Mittenwald to see if an IC/E journey would save you considerable time versions regional trains, but I'm guessing probably not and you'd be better off with those day trips using a Bayern ticket or point-to-point tickets purchased in advance.

You could try to source cheap point-to-point tickets for one of the closer aspects of the trip and get away with a 5 day twin flexi pass for 340 euro, or you could splurge and buy the 7 day pass for 425 (again though, this would mean you are spending an extra 42.50 per person for a day of travel that you could probably get for half that cost with advance tickets or a local day pass) but by all means the 15 day pass at 750 is a huge waste of money for your trip.