I haven't been to Annecy or Vecors, so I can't comment on them, but I've been to Beaune, Dijon, Grenoble, Lyon (at least 3X) and Paris (7X), so I would pick option (C), or a version thereof. I think 3-4 nights in Grenoble is just right - you could certainly do 3 and add another night in Dijon/Beaune as they're both worth 2 nights. Grenoble is wonderful: small, compact, beautiful and with great hikes available. As you may be aware, there are cable cars available that take one up to the mountain fortress/Bastille/citadel that overlooks the City. Not only does it provide great views, but also great hikes. I found the food there to be excellent, with a bit of an Italian influence. The river Isere weaves right through the City and provides great views and walks. Finally, there was a very, very good museum of arts as well as a Museum of the Resistance. They're not the Louvre, but were a surprise to find in Grenoble.
I think Lyon is one of the most underrated treasures of France: lots to do and see, great museums, great roman amphitheaters, the Church of Notre Dame, the Old Town, and unbelievable food. I love that City.
Dijon and Beaune are both very small and both very walkable. Unless you're huge wine fans, the only "must" see in Beaune is the Hospice d' Beaune. But the City has GREAT restaurants. Even if you're not a wine fine, you guys could certainly rent bikes and go for beautiful rides through wine country/vineyards which are literally ten minute rides from downtown.
Dijon has more to do than Beaune, some nice museums, churches, etc. Like Beaune it is in the heart of Burgundy and was the capital at one point, so it has plenty of Escargo, Coq au Vin, Beef Bourgonion (sp.?). Similarly, bike rentals are available to get you into the vineyards. Again, if you're not a wine fine, I would do two nights in Dijon and skip Beaune.
Good luck and best wishes: it sounds like a hell of a trip, regardless of which option you choose.