3 days from Freiburg to Frankfurt. Itinerary help?

Rothenburg is also super touristy. Charming, but lots of people. I don't think Heidelberg is any more touristy than Rothenburg, perhaps less. We spent about a half day in Heidelberg and enjoyed it. Its a pretty city situated on the river with an interesting castle.

I suggest Trier and Cochem. It might be a ways off your “beaten path” but very well worth it.
From Freiburg head north on to Ettlingen West. From there take the L605 to Karlsruhe. From Karlsruhe head to Bad Durkheim. From there you have the option to head a little more north to the famous city of Worms (Martin Luther) just west of Mannheim from Bad Durkheim you’ll head west to Frankenstein and eventually Kaiserslautern. This stretch is one of my favorites drives. From Kaiserslautern you’ll head west to the old Roman city of Trier.
Trier is an amazing retreat to see old Roman baths and amphitheater as well as more traditional post card German structures. From there you can head north to Cochem castle in Cochem off the Moselle River. You can take a historic tour of the castle and is fun as castles go. But the real treat is the wine shops in town. There are also Moselle River boat tours to be had as well. From there head to Frankfurt.
Be warned, Trier and Cochem can be really busy with tourist traffic especially at peak season. Not quite the small quaint towns you were wanting but just a suggestion as a possible option.
Best of fun!

Rothenburg is probably 10 times more touristy than Heidelberg. If you are going by what Rick writes about Heidelberg, remember he wrote this about 30+ years ago. It is a lovely town with plenty to see and certainly not over touristed.

Have you thought about visiting Esslingen? What about Speyer? They are on your way up towards Frankfurt. Würzburg is in the wrong direction. If you want to stay close, consider one of the towns on the Rhein, like Eltville, or up at Eberbach Monastery.

Why would you take that route? It's much too long and really not a good drive. You can do better.

Take the German Wine Road (Weinstrasse). Visit fantastic places like Neustadt (on the Wineroad), Speyer, Bad Durkheim, and Mainz. Detour a bit and see Trier and Cochem on the Mosel. Visit Heidelberg, it's worth it, and the only place you'll really notice tourists are at the castle.

There's a winefest in Bodenheim next weekend. And in Koblenz and Oberwesel on the 7th. And Bingen and Remagen on the 15th. And I'm pretty sure there's some I missed, as the season is on us.

This route will give you better castles (Cochem, Hambach, Wachenheim, Heidelberg, etc.) Drive up 65 and you see one every couple miles.

Plus, and this is a big deal unless you actually like sitting in the car, it's a lot shorter drive.

One morning I was walking along the river in Heidelberg. We saw one man and two dogs. Just one man and two dogs. Through into the centre and a few handfuls of folks... a few hours later and up the hill and there were more, but nowhere as many as in the much smaller Rothenburg odT.

But the two are chalk and cheese. Very different. Both very nice places and both well worth a visit.

As you will be driving, leave enough time to find parking in Tübingen. Roads are narrow there, and the hills are somewhat steep so finding parking may be challenging. It was for me.

I would follow KGC's suggestions for the Weinstrasse or some alternative, more direct route. The detour you are taking to travel to Rothenburg and Würzburg adds unnecessary driving time if you want to experience small-town, old-world Germany. The towns I'll mention below and the ones KGC has mentioned already are very nice places that are NOT mentioned in Rick's book, but I would not let their absence from his materials drive me eastward into Bavaria.

I would not suggest the additional driving needed for Trier, the Mosel River, etc. There's plenty right in between Switzerland and FRA for your short time.

Freiburg and Würzburg are not small towns, btw. Suggested revision:

Sunday:
Gutach/Vogtsbauernhof
Gengenbach
Schiltach

Monday:
Tübingen
Esslingen

Tuesday: More Neckar River towns, good to have choices:
Besigheim
Bad Wimpfen
Burg Guttenberg (Haßmersheim) Castle and Falconry Exhibition
Ladenburg / Bergstrasse towns (pick one to the north on this route for your last night.)

If you're looking for a quaint and lovely village, I would recommend Gengenbach. It is located fairly near the Vogtsbauernhof and is utterly charming with beautiful half-timbered houses (it's frequently called a "chocolate box" village). This is one of my favorite places in the Black Forest. I stayed there for 4 nights in 2022 and absolutely loved it. Gengenbach has a beautiful Altstadt, with quite a few restaurants and cafes to choose from. The town church (Saint Marion) is gorgeous, and the medieval gates to the city are really interesting. The Benedictine Abbey is also worth a visit, and behind it are some cloistered gardens that were a joy to wander through. This was one of my favorite places. It was peaceful and inviting and I could have stayed for hours.

Also don't miss a walk through Engelgasse and Höllengasse streets (near the TIC). Here you will find cobblestones and half-timbered houses, flower pots and cats resting on doormats and quaint dolls in the window. I felt like I was walking back through time when I strolled through these quaint and narrow streets. There is also a nice hike you can take that will get you above the town with some absolutely beautiful views of below. The hike ends up at a church called St. Jakob auf dem Bergle that sits above town. The TIC in town will have maps showing you how to get there. The views are just lovely.

absolutely agree with Mardee. Gengenbach one of our favourites.

The St Jakob chapel on the hill is on a minor route of the Jakobsweg, the Kinzigtäler Jakobusweg - marked with the traditional scallop shell marking the pilgrimage routes. You may have heard of the Camino in Spain - this is the German version. The Way of St James, in English.

https://en.wikipedia.org/wiki/CaminodeSantiago(routedescriptions)

https://en.wikipedia.org/wiki/Gengenbach

https://www.stadt-gengenbach.de/kultur-tourismus/gengenbach-blueht includes a town map with Gengenbach is Blooming and photos.

Thanks for all of the suggestions so far. They are very helpful!

Less driving is a lovely idea, so I'm glad to look at that.
I'm going to plot all of these places as favorites on my TomTom Planner to see it all better.

If you stop on Tuesday night in Mainz, and drop the car, you can catch a train direct to the airport from the Mainz station every 15-20 minutes. I highly recommend you do this and then enjoy the morning in Mainz (take a walk along the river, or do the morning market in front of the Gutenberg Museum, or both). It's a 5 minute walk from there to the station. You could even go see the Isis temple (Roman); it's free and very interesting. And Mainz is a nice city to walk in the evening.

Go to Speyer. Visit the cathedral where a number of German emperors are buried. Visit the Technological Museum (If you can get out of there in less than 4 hours I'd be amazed.) Sit on the river at a beer garden and do lunch.