I think you just said your plan -- you are most excited about Colmar and Marseille, so start by planning your trip there. Take the train from Paris to Colmar to eliminate some driving. Possibly take train south as well. I think a better base would be Arles or Avignon, or there a variety of other smaller places as well.
I have 2 teens and we have done 3 European trips with them starting when they were 12 and 14. My general guidelines are 1) try to limit drive times to 2-3 hrs 2) don't pack too much in 3) stay in villages or smaller towns (few restaurant choices make for easier consensus on where we eat), 4) try to stay 2 or more nights in a place. I have boys -- Roman stuff is always a hit. Battlefields are a hit. So are castles. Picnics are good. Hiking is good. We don't do decorative arts. :) I try to visit things they like and keep things varied.
I think you will have a great trip. But I would skip Pisa for sure, and I would skip Nice and other places you have been. Explore new places together! Also, don't feel you have to spend a lot of brine in Paris. We spent 3 nights which was enough as a family. My boys have the rest of their lives to go back and see it better! Of course, I hope to go back again myself!
RS guidebooks are pretty reliable. I find the towns to be as described.