12 day Switzerland itinerary help

we are not keen on taking overnight trains

No worries mate! There aren't any. Switzerland is not big enough to make these useful.
Download this rail map of Switzerland if you need ideas.
https://cdn-doc.myswissalps.com/docs/default-source/rail-network-maps/swisstravelsystem.pdf?sfvrsn=7788603a_36
Timetables and route planner at www.sbb.ch/en

Plenty of time to fine tune your itinerary. One suggestion, start in Montreux instead of Geneva. There are TGV's from Paris to Lausanne, then a short train ride to Montreux or Vevey. This is wine and chocolate country. Take the Chocolate train to Gruyere (cheese) and Broc (chocolate). Oh yeah, Chillon Castle on the lake.

The other rec is to take the Bernina Express to Tirano, then a local train to Varenna on Lake Como. A short ferry boat ride to Bellagio. There are several ways back to Switzerland without back tracking. Take the ferry across the lake to Menaggio, then bus to Lugano, then train back over the Alps. Specify "via Goeschenen" so you don't have to use the new 50 km Gotthard Base Tunnel which burrows under all that alpine scenery. Or take a fast boat from Varenna to Como and then a taxi or city bus to Como San Giovanni station for a train to Lugano and north.

Thanks for your reply, that is exactly the kind of help I am looking for! I will have a look at skipping Geneva and starting in Montreux, wine, cheese and chocolate sound like my kind of thing.

Have you ever taken the Glacier Express, if so did you think it was worth it?

Rent a car. You will probably save money, but most important is the flexibility you get. Michelin Green Guides are essential for EU road trips. The Green Guide lays out a number of itineraries with basic maps, but you also need a good road map, preferably 1:200 000 but at least 1:500 000 I have never seen an Internet map or GPS that I would consider using for driving around Europe.

Chillon Castle in the lake; 3 passes tour. Easy walking access to a glacier if global warming hasn't killed it; Lauterbrunnen Valley-- Trammel Falls, a waterfalls inside a cave, incredible racket; train via Wengen to Kleinescheideg. Walk over to the cliff and watch avalanches fall down the North Face of the Eiger (watch the Clink Eastwood movie pre-trip); Murren cable car-- top was a big setting for a James Bond movie, another pre-trip film.

St Gallen is far and away the only major city worth a visit: old town & the Baroque Abbey. If you have never seen a Baroque church, you are in for a major surprise. There is nothing like it, and ST Gallen has a good one. Also visit Lake Constance: Mainau Island (palm trees) and take the ferry across to Germany to Meersburg & Lindau (a free city completely covering a little island) If you really liked St Gallen's baroque church, there are a handful of other good ones just north and north west of Lake Constance (Again, Michelin Green Guide Germany is essential)

Having traveled many times to Switzerland with my kids, here's my 2 cents:
Get to Lauterbrunnen, Murren, or Grindelwald and get your family on the trails. Great sights, playgrounds here and there, and cows and goats to pet. Click on my name and you'll see the link to our dozen favorite trails in the area, with maps and pics.

Have you ever taken the Glacier Express, if so did you think it was worth it?

Yes, it was fabulous on a clear winter day with bright sunshine and plenty of snow. Was it worth it? Absolutely, since it was prepaid as part of a travel junket.

Thanks for all the replies. I think we are going to settle in Interlaken for a few days and hike and kayak and then take one of the rail trips and head down to Como. I really appreciate all your help.