best base(s) in fench Alps ?

Stay in Chamonix instead of Annecy which will give better access to Aiguille du Midi Gondola, train to Montenvers, Le Brévent Gondola and the La Flégère Lift.

If I wanted to stay in the Annecy area, I would stay in a village on the eastern side of the lake, like Talloires. Gorgeous views.

I think two nights is short for Lyon. It's a large city with a lot of sights. However, if there's not that much there for your family, that's a different story. You're planning to cover a lot of ground and cannot spend extra time in all of those places.

Chamonix. It's got a cool vibe from all of the hikers/climbers etc. Spectacular views. Annecy is pretty but it is not yet in the "mountains". Get a lift pass for the number of days in town (it will almost pay for itself after 1 trip up to Aiguille du Midi). I would say that most of the hikes require a bit of effort except for the valley hike which is flat and very nice. Also, you will get a train pass from the hotel which gives you access up and down the valley. I could spend alot of time in Chamonix!!!

I really, really like Le Grand-Bornand and La Clusaz as bases between Annecy and Chamonix. I am not 100% objective as part of my family is from that area, however I do think that they would fit your requirements. There are great mellow hikes in the area with some good views of the Mont Blanc massif (e.g. from Col des Aravis or from Beauregard Plateau), lake Annecy is 30-40 minutes away, and the villages in the area are quite charming. Chamonix is 1.5 hours away so a day trip there is feasible.
There are several hotels as well as tons of self-catering accommodation; these are popular ski resorts in the winter.
Otherwise, Talloires mentioned above is a great idea as well, and check out Hotel Les Grillons a few km south in Angon.

As for Lyon: I personally think that 2 nights is enough in a family setting, especially since the drive from Le Puy takes only 2 hours!

I stayed in Chamonix and was happy with it. I rented a car in Lyon because the train through Annecy to Chamonix wasn't at all convenient.

I would also recommend Chamonix. It's a beautiful smaller town with some nice hotels and restaurants, and there are lots of activities to keep you busy. Check the RS France guidebook for more details on activities, but a few to consider.....

• Take the cable cars to the Aguille du Midi on the top of Mont Blanc. While there you can try the Step into the Void, which is a glass platform with nothing below except a 1000 metre drop. One point to note is that the Aguille is at about 12,000 feet so if anyone has altitude issues, you might want to have a chat with your doctor about that.
• Take the Panoramic cable cars from the Auguille across to Pointe Helbronner in Italy.
• Visit the Mer de Glace (Glacier)
• For the adventurous adults, there's also Paragliding.
• Hiking

Thanks for all those ideas !
Never been in very high mountains ( Highest was canadian rockies and Dolomites) so we dont know if it could be a problem.

For now we have made a reservation for an appartment in Thônes. We chose that place because it ‘ a not too far from Annecy, got some restaurants/bakeries/groceries and roads !

And if you been to the Canadian Rockies, then you are being modest about not having seen mountains! IMO those are not surpassed for beauty or majesty by any others. Equaled but not surpassed.

You are stoked to have a car. Chamonix is a good place with some good views of the big mountains, but I wouldn't drive there, park and stay. That's what you do by train.

If you want to go a bit farther afield, drive past Chamonix up over the pass at Le Chatelard and down into Switzerland's upper Rhone valley. From there you're an hour from many cool places - Visp's highest vineyards in the world and the incredible traditional village up in them, The crazy rock formations above Sion, etc.

You can't get more scenic mountains than the Dolomites so not what you are expecting of the Alps
July/August worst time to visit alps as height of French Holiday season

We know that the Rockies and the Dolomites are wonderfull like not many places on earth and we wont expert to see better in France. We just like mountains vibe !

Of course travelling in France in July-August is the worst time of the year but having kids in school and being a teacher and a school psychologist doesnt give us another option. So between not travelling at all and travelling at peak time we have chose the later !