Mountain lifts

That's quite a lot for three weeks.
For your question, to me it would depend on how long I am in each of these places and what else I am doing. I've only been to Luzern from this list. Note you can also take the cog wheel train to Mt Pilatus, which is a unique experience if you are not taking one anywhere else.

I would like to second the trip up Mt. Pilatus, you can take either a train or a lake boat to the base where the cogwheel begins, then it is a beautiful ride up to the summit. Once at the summit you can either go back down on the cogwheel or take the gondola down the other side, half way down there's a nice restaurant and several activities to do (like lunge ride, etc). The gondola is large and can take 20+ people so even if you don't like heights it shouldn't bother you. Your going to have a wonderful time, we loved Switzerland on our Rick Steves tour, and can't wait to go back!

Thank you, valadelphia and Donald. I was thinking of taking the Silver Round Trip itinerary for Mt Pilatus, which means the cog train up and then the lift/gondola down. I'm leaning towards going up to Ebenalp as well to visit the Aescher restaurant/inn and then skipping the Lugano and Pontresina lifts in favor of more downtime between scenic (but long) rail journeys.

valadelphia, I'm largely following the RS two-week itinerary here https://www.ricksteves.com/europe/switzerland/itinerary but added a few extra days (1 overnight in St Gallen, and 1 full day each for Lugano, Lausanne, Bern, and Zurich).

Yes I figured there were some one-night stays in there. If the pace works for you, go for it!

Just 1 one-night stay, actually (St Gallen as I'd like to see the abbey library and textile museum). Everything else is 2 nights or more.

Regarding staying in all those places: do not forget that Switzerland is a small country with a nation wide mass transit system. Bern, Zurich and Luzern are all within one hour of each other. So you can easily base yourself in one place, and do day trips to the other.

St Gallen as I'd like to see the abbey library and textile museum

I was in St. Gallen last Sept. and the library is super impressive. Just note no photos or videos are permitted inside.

St. Gallen has a great old town. Be sure to check out the bow-windows if you have time.

Muottas Muragl is beautiful, and the lift is a funicular railway so you do not leave the ground! However, you have to pay for it - there are no pass discounts.
Can't comment on the suitability of the others for fear of heights - Pilatus might be scary in some respects, but it is hard to assess for others!

WengenK, you make a good point about switching to more of a daytrip-oriented itinerary. Besides Zurich, Luzern and Bern, are there any other stops you'd recommend consolidating? I think the RS itinerary is based on the Grand Train Tour route (albet in reverse), which is built around four scenic rail journeys (Gotthard, Bernina, Glacier, and GoldenLine) which is great as I like trains, but my sister would probably prefer fewer packing/unpacking cycles.

Carrie and balso, thank you. I am excited to visit St Gallen!

I am scared of heights. I have not done any of the transits you have listed but I have gone to and stayed in Muerren which is just gorgeous. There are 2 ways to get to Muerren but I am guessing you will be taking the train to Lauterbrunnen then taking the gondola up to Grutshalp and then the small train to Muerren.

My "gondola" strategy is to try and get on first and if there are benches around the car, immediately sit and close my eyes. If there are no benches (some do, some don't) then I will either stand in the middle of the car if there are a bunch of people around me so I can stare at someone's back or back to the edge of the car and close my eyes.

I don't have any problems with Muerren as I'm good once my feet are on the ground. If you are going to do some hiking, the funicular up to Almendhubel is very easy and the hikes back down are doable. If you are going to the Schilthorn, again , no problem once my feet are on the ground and I could stay far enough back from the rails on the viewing areas that I was fine. 2 Gondola segments up from Muerren to Schilthorn.

In Luzern you could also consider the Rigi (https://www.rigi.ch/en) as an alternative to the Pilatus if you have height issues.