Where to stop on the way from Paris to Munich

I would look at either Freiburg im Breisgau, which is in the Black Forest, or Heidelberg. Neither are small towns but both are university towns with nice old town areas and Heidelberg has a castle also. I preferred Heidelberg myself, but that's just personal opinion.

For "small town scenery" I would probably forego Heidelberg and Freiburg (with populations in the neighborhood of 200k) and instead target places like Gengenbach, Gutach, Schiltach, Haslach, and other towns on/near the scenic Black Forest Railway. One of the main Paris-Munich train routes takes you there via Strasbourg and Offenburg (just across the French border) where the BF Railway begins. From Offenburg, Gengenbach, an old walled town and a good base for short outings) is only a few minutes by train. The other "-ach" towns I named above are close by and easy to reach by train.

Rail map of the Black Forest Railway, not all rail stops are shown

This free train pass for use on outings on the BF Railway and all around the Black Forest is provided to all overnight guests in Gengenbach and certain other BF towns.

Gutach's Open-air museum (Vogtsbauernhof)

Schiltach

Haslach

After your two days here, you catch a train back to Offenburg and move on to Munich as you would have had you never gotten off. Very easy.

If you want to go super-rural, stay in Gutach, where there are several farmhouse accommodations like the Rotbauernhof:

https://www.rotbauernhof.de/php/allrotbauer_haus.php?titel=Ferienwohnungen%20Rotbauernhof&max=18&pfad=haus

I presume you are spending a few days in Paris, otherwise the air routing seems odd. I don't think that October is ideal for the Black Forest, but I can't say exactly when the leaves there start to fall. I would point out that hiking is harder with roots and stones hidden by leaves. (I'm not suggesting that the trails are poorly maintained. I'm talking about October.) If hiking (simple, moderate, or strenuous are all available) is important to you, I would rather stay in a town (not Freiburg) which offers KONUS transit cards free with hotel rooms. That makes daytrips easy and free.

It is debatable (!) whether the BF is more attractive or less attractive at the peak of summer tourism. (Ironica typeface.) Because I like urban tourism too (like Freiburg), you might consider Strasbourg as an obvious stop from Paris. Open air daytrips may be do-able from there. It is possible to TGV to Strasbourg directly from CDG if that is what you are actually doing. It is more out-of-the-way, but Basel has some fine museums.

If hiking is not important to you, there are plenty of attractive small towns to visit in Bavaria, as well as elsewhere in Germany. Because you asked, I will say that I stayed at a luxury resort in Hinterzarten, which might be affordable off-season like this. I took the (free) train to Titisee (mass tourism destination) and walked back to Hinterzarten. Another day I trained to Freiburg for the day. Parkhotel Adler is an easy walk from the train.

Thanks so much for the ideas....very detailed. Will have an adult son with us ....will there be enough "entertainment" (dont know what to call pubs in germany)?

Probably don't require too many pubs (Kneipen) for such a short stay. Munich and Paris have them in the hundreds of course.

Gengenbach: Leaf through the photos and check out the food and bar at Zum Turm. There's also the Frei Steinkellerhaus