Traveling from Arles or Marseilles to Switzerland, Itinerary for France Trip

You can see the train lines into Switzerland from southern France on these maps:

https://www.sbb.ch/content/dam/internet/sbb/en/freizeit-ferien/inspiration/internationale-gaeste/Geltungsbereich-Swiss-Travel-Pass.pdf.sbbdownload.pdf

There are very few, because of the Alps. The only direct train to Geneva comes from Lyon. So from Marseilles, you would change trains at Lyon. That is probably the simplest choice (fewest transfers en route).

Indeed there are no direct trains between Provence and Switzerland, but the transfer in Lyon is not much of a hassle. The end of the route from Lyon to Geneva is pretty, but not that scenic. There are no scenic alternatives.

As for your route, I think it is a bit fast, especially the Sarlat bit. I would consider skipping touristy Mont St Michel and staying 4 nights in Sarlat instead. Or if you must, then just 1 night in Mont Saint Michel.

Arles is closer to Avignon than to Marseilles. And it is in more the "right" direction to Geneva. You could train to Geneva from Avignon with only one change. Avignon TGV station is outside the city and easy to access by car for your return. Or you could bus from Avignon with no changes. Look at options on rome2rio.com. That is a good website to start the journey planning but do check any options then directly on other websites. Others can advise if train or bus would be scenic.

There are direct local trains, called TER, from Arles to Lyon. You don't need to go to Marseille. Other routes have you taking a TER to Avignon, transferting to the Avignon TGV station, and then zipping to Lyon. One other route has you changing trains in Valence to a TGV. So you have plenty of options for getting to Lyon to catch the local train to Geneva without going out of your way to Marseille.

Thanks everyone for your responses - this is really helpful! I decided to adjust our stay in Mont St Michel to 1 night and add another night to Sarlat. Really excited for our trip!