Cont. First Time to France - need help with itinerary - UPDATED with our thoughts

You might want to cross-check your estimated driving times and suggested routes with ViaMichelin.com. It may not differ much from Google Maps (if that's what you've been using), but it has the advantage of highlighting scenic roads in green.

When planning your sightseeing options at each stop, keep in mind that 3 nights is not 4 days; it is two days plus some random hours. Three nights may be a bit short for Strasbourg if you want to sightsee in that city and in Colmar, plus visit multiple wine villages and even Germany.

Strasbourg plus the wine villages needs more time. I recommend that you spend at least one night in a charming wine village . We stayed in Riquewehr . Stay in Alsace and skip Germany this time; it used to be part of Germany. We loved Strasbourg, were disappointed in Colmar.

You are figuring your number of days wrong. 2 nights = 1 day, 4 nights = 3 days, etc

The Black Forest and Freiburg are close to Strasbourg if you feel you need to check that box. Have some Schwarzwälder Kirschtorte if you do (Cafe Diva in Hinterzarten is superb). Suki is correct your time can easily be consumed staying in Alsace doing Strasbourg, Colmar, and the wine villages. However, I found Colmar to be a delight. The villages are interesting and worthwhile linked in a day trip. In Beaune, study to make sure that visiting wineries meets your expectations. They are generally not as visitor friendly as in the US and there is an expectation to make a purchase. Beaune wines are not cheap here or there. The Rick Steves Guide's driving tour south of Beaune to Montrachet, Le Rochepot, and Saint-Romaine is a good loop. From Annecy, look at a day trip to Chamonix in good weather rather than a trek to Switzerland. The cable car to Aiguille du Midi is spectacular. Geneva is a snooze. There are some nice wineries on the north shore of Lake Geneva but they are not worth a special trip unless you have a fascination with Swiss wine which rarely is imported here. When you return the car to CDG, try to avoid the Périphérique around Paris. I did it once and have no intention of ever doing it again. You are assembling a nice trip.

Hi-wow, sounds great! For transport from CDG to your hotel, you might check with them and see if they have a pick-up...I have experienced good service and reasonable pricing. However, there is also the taxi stand at CDG...I am just a sucker for pre planned transportation to my hotel/apartment. Also, regarding Strausborg, which is a charming walkable city/town, you are close to Colmar for a drive as well as Kaysersberg. I am certain your hotel in Strausborg can assist. Just a suggestion..

As acraven pointed out, your nights/days calculation distorts how long you'll be in each place -- unless you've figured out how to live through consecutive days without spending a night between them. ;-)

Coming to Paris from Bourges, you might want to drop off the car at Orly, the airport on the southern outskirts of Paris, to save time and driving hassles. There's a shuttle from there to the Metro, or take a taxi to the hotel. No need to circle halfway around the big city.

Why is it recommended to drop off your car at the airport? Is that so you don't have to drive in Paris? At any rate, if you drop off your car at the airport, I strongly recommend taking a taxi directly to your hotel. That's what we did and the cost was around $50. It's just so much easier when dealing with luggage.

You don’t need to drop off car at CDG. There will be an extra airport fee. It’s very easy to drop off at Orly airport. Or you can drop off at a railway station. Pick the one closest to the highway you will be traveling on near Paris.

Bourges adds significant driving time on some not-so-fast roads. Vichy is quaint for sure, but some would say "faded"; if you want to visit a 19th c. French thermal resort you have Aix les Bains right next to Annecy.
I would be inclined to skip Bourges and add a night to both Strasbourg and Annecy. Driving from Strasbourg to Annecy, then Annecy to Beaune.

Edit: misread the nights; the Vichy night could be spent in Beaune (there are many sights in Burgundy), or you could break the drive between Strasbourg and Annecy with a stop in cute Baume-les-Messieurs or Arbois, villages in the Jura region.

We recently did a 24-night trip to France that included Beaune, Colmar (day trip to Strasbourg), and Paris. Here are some things we really enjoyed:

Beaune wine tastings:
- Domaine Lejeune in Pommard. We walked from Beaune to the winery in about an hour (with a 4 year old toddler moving at a leisurely pace). The walk is very scenic (through vineyards), and the town of Pommard is very cute. We loved our wine tasting at Lejeune with the husband of the current owner (it was a private tour with our group only - make sure you reserve ahead of time).
- Domaine Francois Buffet in Volnay. This winery had our favorite wines of the whole trip. Again, it's a private tour so make sure you reserve ahead of time.
- Patriarche Pere et Fils in Beaune. This was our favorite setting for the tour - the underground cellars are incredible. Our wine tasting took place by candlelight. They buy barrels of the famed Beaune Hospice wine, which was really cool to see and hear about. We had advance reservations although this is a bigger operation so I'm not sure that's completely necessary.
- Philippe LeClerc in Gevrey-Chambertin. This was not our favorite tour/tasting, so I wouldn't say go out of your way to visit, but you can just drop in, so it's convenient if you're in the area.

Just one thing to add about "passing through" Lyon - we started our trip there (before renting a car) and everyone agreed that we were so glad we hadn't rented a car in Lyon! It's a big city with a lot of very narrow one-way streets, plus bikers/pedestrians/other cars to think about. I wouldn't go through the hassle of stopping in Lyon with a car; I'd just keep driving and stop at a smaller town nearby for lunch if you need to.

Yes, drop the car at Orly and take a taxi to your hotel. Taxis are fixed rate and for the two of you, not much difference in price from taking public transportation. .
I like the idea of Bourges, truly deep into France. It's not on the US tourist-track but has a lot to offer.
I've been to two health spa towns in the Massive Central area, including Vichy, and find them sad. It wouldn't be my first choice.

Also did the Patriarche underground tour in Beaune, by contrast we were left all on our own, going from small room to small room to self-sample, until the end when a hostess popped up and wanted to know how many cases we wanted to purchase. We told her frankly we didn't care for the wine and she sniffed away.