Laurel, thanks again. FWIW, I use R2R to get a visual idea of how the various destinations could be stitched together (a bit like Google Maps, but with trains and buses as well as roads), but then I switch to SBB or one of the other train sites to flesh out the actual time tables and connections. I am impressed with SBB-i especially like the detailed route and station maps that pop up for each train itinerary, which then tells me if there are any interim stops I should consider between points A and B. Trainline gives me a quicker answer for fares but doesn't have the visual tools like SBB, which IMHO is the best train site available for Europe.
Zermatt seems like the riskiest destination on the itinerary; it is a strategic location for the Glacier Express, but since we will be traveling on other scenic routes (Panorama, Bernina, the Golden Pass if we add Montreux, the Voralpen between Lucerne and St Gallen), I am okay with giving up the Glacier Express and dropping Zermatt. In fact, if I substitute Montreux (or Lausanne) for Zermatt, we get a more balanced itinerary, one that more evenly splits our time between mountain towns and cities (which Mrs W favors).
Berner Oberland should be fine, although Lauterbrunnen might work better in the face of variable weather; then if the weather turns bad, we can take a day trip to Bern (maybe even Gruyeres) for some indoors sightseeing (or at least walking paved surfaces in the rain). We won't get the spectacular views from our room like we would in Murren or Wengen and the cable cars will be less accessible, but that seems like a minor inconvenience. However, after looking at some of the places we could stay in Murren and Wengen (and the amazing views from the hotels), that may be easier said than done!
Substituting Montreux or Lausanne for Zermatt will give us exposure to the French side of Switzerland, and St Gallen could be a good substitute for Appenzell, which would also give us easier access to a rental car if we want to drive to some of the nearby towns (Lindau across the border, maybe even Lichtenstein). Lucerne seems like a good candidate for more time for day trips or additional sightseeing in the city and surrounding area.
So with those changes, the itinerary looks like like this:
Menaggio-3
Lucerne-4
Lauterbrunnen-4
Montreux-3
Sankt Gallen-4
Pontresina-1
Milan-3
Not counting Menaggio and Milan (which offset each other for the outdoor/city split), that gives us a roughly 50/50 split between cities and mountain towns, which I think is a good approach for hedging our bets on the weather and trail conditions. It drops the Glacier Express but includes four other scenic train routes.