Oh, I liked Cahors!
If you search for train routings between Toulouse and Lauterbrunnen, you'll find some run through Montpellier and some shoot north to Paris. At least some of the trains on the Parisian route stop in Strasbourg (or that might be one of the transfer points), so stopping there wouldn't add much time to the trip, but it is a long slog from Toulouse to Strasbourg; it's nowhere near the mid-point of the trip.
In that regard, Lyon fits better, but it has more than 1.5 days' worth of sights--a very large number of good museums on a wide variety of subjects, Old Lyon, and the Presqu'ile area. Google museums Lyon for a quick look at the museum options. Really, Lyon is sort of a mini-Paris. Unless you hate museums of all types, you'll need to move rapidly to get a decent look at the city in the amount of time you will have. I spent several nights there but only scratched the surface. I liked the Resistance Museum, the Textile Museum, the Decorative Art Museum and the Museum of Fine Arts. Others have spoken highly of the the Confluence Museum (science and anthropology), the Gallo-Roman Museum and the Cinema Museum. It's a really interesting city with a lot to offer.
I haven't been to Chamonix. I thought Annecy was a gorgeous town in a gorgeous setting, but it was incredibly crowded in June 2017. It was also terribly hot, and many of the budget-level lodgings are not air conditioned. Chamonix is at altitude, so heat probably wouldn't be an issue there.