Patrick, you don't visit Switzerland for cities, you visit it for mountains. I would skip Zürich and Geneva, and do Bern as a day trip from the Jungfrau region (Mürren), on whichever day has the worst weather. I would also do the trip as a big circuit, so you can get in at least one of the most scenic rail route. You say 2 weeks, that would be 13 nights in Switzerland.
My suggestion would be:
- Land Zürich, immediate train to Chur. 1 night (this is a positioning move, but you will see lots of mountains on the way).
- Glacier Express route to Zermatt. 3-4 nights
- Train to Montreux. Visit Château de Chillon, walk vineyards. 1 night.
- Train to Mürren, via "Golden Pass" train. 3-4 nights. Alternatively Wengen, Lauterbrunnen or Grindelwald. Use a bad weather day for Bern.
- Train to Luzern. This is the scenic Brünig pass route. 3-4 nights. Boat trips on lake. Trip up local mountain. Possibly day trip to Basel, but you might run out of nights.
- Train from Luzern direct to Zürich airport, only 70 minutes. Fly home.
You can trace this route out on the Swiss Rail map here: https://www.sbb.ch/content/dam/sbb/de/infotexte/uebersichtskarte-sts.pdf