Is this 3-1/2 weeks in France a segment of a longer trip? Are you flying to France from the US or Canada? Where are you heading after France? It appears you're not going to North America, based on your 9 PM flight-departure time.
Is this your first trip to France?
Although I've been to all your proposed destinations except Chamonix, I have never been to Europe in the winter, so I do not speak from personal experience with December conditions, but do keep the possibility of wet or snowy weather in mind, as well as the certainty of short days, as you consider the pace of your trip. You simply will not have as many daytime sightseeing hours available as a summer traveler would.
In terms of transportation time, Annecy is closer to Chamonix than to Lyon, so if you're staying in both Lyon and Chamonix and want to see Annecy, it seems it would be better to day-trip there from Chamonix. However, it your lodging costs are much higher in Chamonix, that could change the calculation.
If by "drop by Nice" you are suggesting a day-trip from Marseille, I'd definitely discourage it. There's no TGV line from Marseille to Nice, so the trip takes over 2-1/2 hours each way.
In terms of the overall picture, you have an unusual distribution of time: Only three full days in Paris (have you been there before?) yet two full days in Bordeaux and Marseille, neither of which has a fraction of the attractions available in Paris. I thought Lyon was more interesting that Bordeaux or Marseille, and I'd definitely add a day there if you decide to take a day-trip.
Bordeaux is especially problematic here. It will take nearly 6 hours to get there by train from Marseille. A major reason to go to Bordeaux is that it's near the Dordogne, but you don't have the Dordogne on your itinerary and December is probably not at all a good month to be there. I'd scratch Bordeaux entirely from this trip and limit your itinerary to eastern France. Western France has lots of points of interest, but you cannot cover the entire country in a reasonable fashion in 3-1/2 weeks.
Are you aware of the mistral? If you run into it, it will negatively affect enjoyment of outdoor time in Provence (the trip segment from Avignon/Aix to Marseille). The Riviera (coastal stretch on both sides of Nice) would be safer, weather-wise. There are some nice towns there. Lots of art museums, but you didn't mention art among your interests, and the Roman ruins are in Provence.
The time in Alsace feels rushed, though I don't know what the area will be like in December. The first change I'd make would be to take a train to Strasbourg or Colmar on your arrival day. To keep the rail fare reasonable, you'll probably need to buy the ticket well in advance, which will be a bit of a gamble if you are flying in. Leave lots of time between scheduled flight arrival time and train departure time.
We have some folks on the forum very experienced with traveling or living in France. I trust they will provide their very valuable input soon.