Feedback on proposed itinerary

Welcome pr2000! You'll to see a lot of the country with this itinerary. It does include quite some traveling, but I assume you're fine with that since you're all into trains. Adding in the Glacier Express would make the journey more hectic and would allow less time in one of the resorts you've listed, and it's a matter of personal preference whether or not you're fine with that. You'll have to change your travel scheme in order to fit in the Glacier Express, but it's doable: get to Chur or St. Moritz right away from Zurich and make the Glacier Express trip to Zermatt the next day. Then, continue your itinerary as planned with one day off your time in Zermatt, Wengen or Lucerne. Making the Bernina trip to Tirano and back as well would require an additional day of traveling from Chur/St. Moritz. You can plan all trips with the aid of the timetable.

As for missing out on big things: there are so many highlights that it's impossible to cover them all in a relatively short trip. You will get to see a lot though, so don't worry about that. Personally, I'd prefer to focus on the Lucerne region while staying there instead of making a day trip to the Rhine Falls. You may want to see if you can plan the Rhine Falls shortly after arrival or before departure to/from Zurich, which allows you to spend your time in Lucerne and the Lake Lucerne region. Consider, for example, a visit to Rigi or Pilatus if weather is clear.

Also see if you can list some bad weather alternatives. Train rides are always an option, but you don't want to spend your money on viewing points only to end up in the clouds. There are lots of museums in Zurich and Lucerne, for example. Boat rides and the open air museum in Ballenberg are worth considering too.

I think you should look into rail passes in order to save money. Depending on your final itinerary, a 3, 4 or 5 day Swiss Saver Flexi Pass might be the best solution. Free entrance to many museums is included and your child travels along for free on all trips.