itinerary suggestions

From Chamonix to Lyon, then either of these:

(1) If you've been to Paris and don't want to spend time there, rent a car in Lyon and drive into Burgundy for several days, then maybe Alsace or Champagne. Drop the car near Paris, or right at the airport if you're flying out. (But don't plan to drive very far on the day of your flight, stay at or near the airport instead.)

(2) Otherwise, take the fast train (Inoui) from Lyon to Paris and spend your week there.

Great suggestion. I misspoke earlier as we will be there the last week in October. We have been to Paris so
smaller towns are very attractive. Is it a good opportunity to see fall leaves changing?

In the last week in October, you might still have some fall colors in the Beaujolais vineyards and perhaps southern Burgundy (Mâcon / Tournus), but not further north. Tournus is a good base to tour the area (Beaune, Cluny, Autun...).

Thank you for your suggestions.
Do you have any favorite vineyards or sights in those areas?

We are flying into Frankfurt and leave via Geneva a week later. Does anyone have suggestions of highlights to see between Frankfurt and Geneva? We plan to drive and would like to see Chamoniox as well. Any suggestions would be greatly appreciated!
Thank you

Umm, there are more highlights than what I could possibly list!
All of Alsace, western Bade-Wurtemberg (incl. Baden Baden, Freiburg, and Black Forest towns), most of Switzerland... it would take weeks to explore it all. What do you want to see? And I am not sure I would add Chamonix to that route; it extends it even further.

By the way, it is usually expensive to rent a car in Germany and return it in, say, Switzerland or France. Drop off fees are typically somewhere around $600-1,000. Do you have a quote already?