Munich to Barcelona via train, where to stop in route for a couple days?

If you're looking for a single stop I'd suggest Lyon.

Geneva or Paris if you take the long route

I’m not interested in going to Paris and I have been to Geneva, don’t really want to go back, but it is on the way. Lyon sounds like a good a good destination. Not sure about the train route though.

Munich to Lyon can be done with one change in Mannheim, but takes around 8 hours.

Lyon to Barcelona is easy, there is a daily direct high speed train.

If you want to make a stopover in Lyon and avoid Paris, you basically have two options (1) Munich - Stuttgart - Strasbourg - Lyon, (2) Munich - Zurich - Geneva - Lyon.
Connection (1) is 50 minutes faster, but since both Stuttgart main station itself as well as Stuttgart - Strasbourg have major construction sites, it is not sure whether the scheduled 7 minutes changeover time in Stuttgart is sufficient. If you want to be on the safe side, you would have to take a earlier train, which would equalize the difference in travel time. Personally, I would take connection (2), which is in any case less stressful. Either (a) Munich departing at 8:54 Zurich arriving at 12:27 / departing at 13:34 Dijon arriving at 15:59 / dep. 16:20 - Lyon Part Dieu arr. 17:56 or (b) Munich dep. 10:54 Zurich arr. 14:27 / dep. 14:32 Geneve arr. 17:18 / dep. 17:29 Lyon arr. 19:23.

I would buy the tickets separately: For Munich - Zurich the DB has favorable saver fares, for Zurich - Lyon I would compare the prices at SBB and SNCF. You can of course also buy everything together from resellers like Trainline if the price is right (but avoid RailNinja in any case).

Danke!! Thank you for the most helpful reply.