My husband and I are planning our first trip to Switzerland in early July. We will be flying into Zurich and plan on taking a train to Lucerne, spending two nights in Lucerne; then on to Wengen via Interlaken on the Golden Pass; four nights in Wengen. Then back to Zurich via Bern, three nights in Zurich. We may, depending on the weather, visit Bern earlier from Wengen, or just break our trip to Zurich and spend a day in Bern on our way to Zurich. I am trying to find a balance between seeing a good slice of wonderful places and having enough time to savor what we see. Too much hotel hopping would allow us to go more places but with less quality time in each. Think we may need to save Zermatt, Appenzell, Lausanne areas for future trips. This is nine nights total, but the first day in Lucerne will be recovering/napping from an all night flight; the last day in Zurich will be just heading to Zurich Airport. Does this itinerary make sense and the best use of our time? Any help will be much appreciated. Thank you.

Your itinerary makes sense. The main problem might be the weather. There is absolutely no fine weather guarantee for early July.
It may be fine or it may be rainy, nobody knows.
Bern can easily be visited on a stop over between Interlaken and Zurich. The railway station (with hand luggage lockers) is in tthe historic city center. Everything can easily be done on foot (although tramways run evey few minutes).
Day trips from Wengen make only sense if the weather is really too bad there. Otherwise you will be fully busy with the Wengen-Grindelwald-Muerren area for 3 days.
Same remark for Lucerne. There are tons of possible day trips (even to subtropical Lake Lugano, 1 hr 40 min by train OW), bu 1 full day isn't even enough for a somewhaat decent visit of Lucerne (1/2 day), the lake (with historic more than 100 years old steamboats) and the surrounding mountains which can be reached by cog wheel railways, rope railways and gondolas.

Thank you! Yes, we are cutting Lucerne short. It was a toss up —I more night in Lucerne or the time in Wengen. Based on comments we dec

How about this:
Day 1. Arrive Zurich in AM. Train to Bern for one night.
Day 2. Train to Wengen for 4 nights
Day 3. Wengen
Day 4. Wengen
Day 5. Wengen
Day 6. Train to Lucerne for 3 nights. Train segment Interlaken to Lucerne is Golden Pass route.
Day 7. Lucerne
Day 8. Lucerne
Day 9. Train to Zurich for one night.
Day 10. Fly home.

hannahbrewer - I think that dugi has got it about right. Some 4 years ago we did a trip very similar to this, except that we flew into Geneva. After spending the night near the airport as we'd had a late arrival, we caught the train to Interlaken and spent three nights there exploring the lakes by boat and also doing a day trip to Bern on the one wet day. We then moved up the mountain to Wengen and were blessed with wonderful weather. There are many options for exploring but our favourite was definitely going up to Jungfraujoch but be warned, to gets very busy and we had to book when we arrived in Wengen for our last day there. Finally we got the train to Lucerne and had 4 nights there which was barely long enough.