Lyon Annecy Chamonix and possibly Geneva

I would travel in the following sequence: Paris-Geneva-Chamonix-Annecy-Lyon-Aix.
It minimizes total travel time.
Assuming you have 9 nights, I would spend:

• 1 in Geneva: a morning train will get you there by lunchtime, and an afternoon is enough to visit the city if you are OK skipping the museums.

• 3 in Chamonix: 2 full days will allow you to do several excursions and increase your chance of good weather

• 2 in Annecy: to have time to see not only the city (a few hours) but also the lake

• 3 in Lyon.

Paris-Geneva and Annecy-Lyon are easy by train. Geneva-Chamonix and Chamonix-Annecy are doable by train too, but buses are faster.

And welcome to the forum, by the way!

I picked up a rental car in Lyon. The train was much less convenient for my plan (Paris, Lyon, Annecy, Chamonix, then south to Provence via the Ardeche), particularly for traveling from Lyon to Chamonix via Annecy. You are spending more time in the area than I did, so it may work fine.

I found the car particularly useful in and around Provence. I ended that trip in the Riviera, so dropped the car when I arrived in Antibes, used the train around the area and caught an Air France back to Paris out of Nice.

I didn't visit Geneva on that trip so can't provide advice on how to tie it in to your itinerary.

I like the number of days Balso allocated to each location. We did Annecy to Lyon to Paris by train and it was very easy. (Our trip originated in Italy.). It’s a beautiful area.