Need help narrowing down cute French villages

last year ( may/june) we drove through that area, driving through and visiting a number of the towns you mention. we stayed in Beaune for a few nights and then moved north west for a few more nights. I would have to consult maps to give you exact details. we found most of the small villages we stopped in or drove through we all but empty of people. ( other than a few tourists and a few locals) while the villages/towns were good to see, it was a bit disappointing to see many shops closed up( eg: closed down) and no activity.
so , its worth asking here for advice rather than relying on just looking at a map.
hope this helps

I've been to all of the towns/villages you list except one (Flavigny ...). Here are my top suggestions, roughly in my recommended order, although they're all so beautiful it's difficult to choose. I'm attaching a link to my travel blog, which includes something about most of these places. If you put them into the search box you'll come up with some pictures and/or some text. https://mainelywinenews.blogspot.com/

Baume les Messieurs
Semur en Auxois
Cremieu
Chateauneuf en Auxois
Oingt
Pesmes

As to what I'd suggest you skip, that's difficult. I know that Perouges is a Plus Beaux Villages, and I thought it was somewhat interesting, but I thought it was overly touristy and a 30 minute walk through it was plenty.
And yes, Cluny is worth a stop. We were there last year, and there are a few pictures in my blog.

Can only give you opinions on the ones I've visited (or at least specifically remember visiting). I used Semur en Auxois as a base and really liked everything about it. I'd go again.

Perouges is a very nice town. I wasn't completely in love with it because it felt, I don't know, inauthentic? It's like they took a medieval town and cleared much of it in order to have broader roads and squares, leaving only the nicer places. Everything is nice/pretty but the roads are wider and squares bigger than normal medieval towns. I'm not sure why?

Oingt is on my list but I haven't been within range to visit yet.

In Burgundy every little town is prettier than the last. Most have some specific claim to fame (church, fountain, gate, ramparts). It's hard to pick one over others.

The place I liked least was Beaune. It's not my place for a few reasons. I prefer medieval, Beaune was completely redone in the 17th and 18th century. The area around the major tourist sights are fairly nice; I tend to walk a lot and the other half of the center is quite run down. I'm not a big reservations person. There are a ton of restaurants in the center; even in May the good ones need reservations. If you see a restaurant that doesn't require reservations, it's probably horrible - I ate some really bad meals in Beaune - have your lodging call to reserve a table for you at someplace decent. My view is colored by my hotel shower having only cold water. The hotel owner had an Italian attitude toward it ("Oh well"). It's one reason I've been leaning toward Airbnb lately.

You can see snapshots of our visits of Semur en Auxois (my favorite of what I know on your list); Flavigny; and Chateauneuf en Auxois as well as Fontenay Abbey here:
https://janettravels.wordpress.com/category/burgundy/
We spent a week in Semur having stopped for a night on an earlier trip; it is just a pretty stunning place and was a good base for the area. We also enjoyed just driving around following signs to chateaux and other sites; sometimes they lead to laughable ruins and other times to small treasures. Beautiful country.

Don’t want to say you have to ignore them, but I would not focus too much on names. Burgundy is almost ideal for spontaneous discoveries like Janet already says. Looking for a sleeping place for instance I discovered Semur-en-Auxois by accident 12 years ago. Driving downhill (D954) from the westside of town I couldn’t believe my eyes….still can remember that moment. Planning makes sense ofcourse, but keep room for some “surprises around the corner” as Burgundy has enough of them. On the way to Vézelay and Guédelon little Époisses was one too for instance.

Loving history: If there is one event that changed the course of history of France (and a lot more) it will be the Battle of Alesia, where Gallic leader Vercingetorix was defeated by Julius Ceasar. There is a “MuséoParc” and a huge statue of Vercingetorix a few km north of Flavigny-sur-Ozerain. Abbeye de Fontenay is stunning and not to miss to my opinion.

A well detailed map can be a good help for planning itineraries. For driving through the countryside I like to use the yellow cover Michelin Departemental (scale 1/150,000) maps with touristic info and suggestions for itineraries. Green ligned roads are scenic, stars indicate places of interest.

We had a lovely and very reasonably priced meal at the Hotel de France in Beaune. I would add Noyers Sur Surein to your list of towns. We really enjoyed the serene, half timbered, medieval village.

I would add Noyers Sur Surein to your list of towns.

I agree, although if you started adding more charming villages in the area to the original list, you'd have pages of them. Another is Montreal, not far from Noyers. And ....