Switzerland Itinerary

My bias is always toward moving more slowly, so keep that in mind here.

There appear to be budget-priced non-stop flights available from both Lisbon and Prague into key Swiss cities (not necessarily every day of the week), so it would be possible to do as you are considering. It would only make sense to make Prague or Lisbon either the first or last stop, however, so check multi-city airfares to be sure you're OK with them.

If I were choosing between Lisbon and Prague for a short city break, I'd probably take Prague. Many people go to Czechia and only see Prague. I can't imagine going to Portugal and seeing only Lisbon (although I really like that city).

Before giving up the necessary four (?) days in Switzerland, though, consider that your priority there is outdoor sightseeing. I've been to Switzerland in June on several occasions (though not recently), and I have experienced a lot of weather that wasn't conducive to outdoor activities--as in four days in a row of chilly rain. The more time you have in the country, the better chance you have of being able to really enjoy mountain walks and the like. On occasion the weather can be so bad--what with a combination of rain and fog--that your really cannot see the view from inside a train. Been there; experienced that.

Why not see more of Switzerland? Zermatt, Luzern, St. Moritz/Pontresina and take one of the scenic rail trips.

Arrive Zurich and immediately take a train to Lauterbrunnen or the little village of your chose, like Muerren. Spend 4-5 nights. Train to Zermatt for 3-4 nights then take the Glacier Express to St. Moritz and wrap up with a few nights in Pontresina. You may have to allocate one night to stay in Zurich before you fly out.

Advocate of staying in Luzern for the last stop and taking a train to the airport (direct, 1 hour) for the flight home. And if arriving jet-lagged, go straight to your first destination and relax there. Geneva and Zurich fall into the category of "Nice place to live, wouldn't want to visit." IMO. I'll leave out the "humble".

It's the Swiss country/mountains that captivate me.

...

I would love to spend a few nights in either Lisbon or Prague

There are no Swiss countryside or mountains in or near Lisbon.

There are no Swiss countryside or mountains in or near Prague.

I agree with you that the beauty of Switzerland is in the mountains. And there is no reason why you can't add Prague at the end or the beginning. Forget about sightseeing Geneva or Zurich.

For example:
Day 1 departing from ??
Day 2: arrive in Prague. Stay in Prague. 5 nights.
Day 7: fly to either Zurich, Geneva or Basel depending on flight availability and your timeline. Train to the Bernese Oberland. If you have never been, it is spectacular. If you have been before, welcome back. I know I don't ever want to leave either. 6 nights in either Mürren or Wengen.
Day 13 travel to Lucerne. Spend last night. If your flight on your last day is in afternoon, it can be easily done. There is a direct train to Zurich airport.
Day 14: fly home

For 2 weeks in Switzerland utilising the Swiss scenic trains ...

Arrive in Geneva
Train from Geneva to Montreux (3N)*
(Day trip from Montreux to Lausanne & Geneva)

From Montreux to Lauterbrunnen (3N)
From Lauterbrunnen to Luzern (3N)
... on the Golden Pass Line
http://www.goldenpassline.ch
(Day trip from Lauterbrunnen to Murren & Jungfrau)
(Day trip from Luzern to Pilatus & Zurich)

From Luzern to Lugano (1N)
... on the Gothard Panorama Express
https://www.sbb.ch/en/leisure-holidays/travel-in-switzerland/panorama-trips/travelling-gotthard-panorama-express.html

From Lugano to St Moritz (1N)
... on the Bernina Express
https://www.rhb.ch/en/panoramic-trains/bernina-express

From St Moritz to Zermatt (2N)
... on the Glacier Express
https://www.glacierexpress.ch/en/
(Day trip from Zermatt to Gornergrat)

Train from Zermatt to Bern (1N)
Depart from Zurich