Unfortunately, with only 3 nights to visit 3 Swiss areas, you'll see most of Switzerland from the train window. There are late evening trains to maximize your daylight hours but few overnight trains.
That being said, I would suggest 1) the Paris-Est/Bern run with one train change in Basel Switzerland or the Paris-Gare-de-Lyon/Bern run with one train change in Geneva. There are a couple during the day. These runs take between 4.5hrs-5.5hrs. Other runs from Paris-Est and Paris-Gare-de-Lyon have more train changes and take longer. 2) Luzern/Bern. This is a 90 minute train ride and usually with one train change. If you plan well, there are a couple of runs with no train changes.
3) Luzern/Interlaken Ost. There's a 7:55 train out of Luzern with no train changes. The trip takes 2.5hrs. I think that there is a Golden Pass train on these tracks as well. From Interlaken, take the 20-min Jungfraubahn train into Lauterbrunnen. You can stay there or in Wengen or Muerren. All great. 4) Lauterbrunnen/Venice-Santa Lucia. This run will take you 8.5hrs. and require 3-4 train changes.
In my opinion, the top of the Jungfrau is a great mountain top to visit. Note, however, that it's 2hrs up and 2hrs back. The cost is $180 round-trip without some kind of Swiss Pass.