Wengen 6 nights, or Lucern 2/Wengen 4

On your first day, it's easy to hop a train and go straight to Lucerne. The train station is at the airport , is easy to navigate, and it only takes a little over an hour to get to Lucerne. We've done it a few times on jet lag, and it works out well.
So I suggest following your first itinerary, but spend three nights in Lucerne. Your son will love the efficiency of the Swiss train system, the boat rides on the lakes, the cogwheel trains, and the gondolas that ascend the summits.
Safe travels !

https://community.ricksteves.com/travel-forum/trip-reports/lucerne-62eb4d28-60ab-4837-b4b4-91a2486eb732

I've attached my Trip Report from our 2021 Swiss adventure. Perhaps there's some useful info included that may help your time in Lucerne and the Berner Oberland.

I also recommend skipping that first night in Zurich and head to Lucerne and spend two nights there. There will be lots to do when you arrive in Wengen and not enough time - hiking near Kleine Scheidegg, hiking in Murren, the Schilthorn, Gimmelwald, Lauterbrunnen, and endless other opportunities. You’ll definitely want to return. I’ll be returning for the fifth time next month.

Lucerne - 2 nights
Wengen - 5 nights
Annecy - 3 nights
Zurich - 1 night

There was a similar question about Lucerne vs. Berner Oberland here:

https://community.ricksteves.com/travel-forum/switzerland/help-planning-switzerland-3-day-itinerary

I suggested in that thread that one could visit Lucerne on that way down to Wengen/Berner Oberland.
In any case, if your boy likes the Alps, you and he can check out the trails in advance at this site:

https://lauterbrunnenhiking.wordpress.com/ All of the trails listed were tested by my kids when they were 13 (and they came back to the same trails as adults).

I agree with the suggestion to head straight to Luzern from the airport. There are 2 trains per hour that go directly from the Zurich airport terminal to Luzern, without a change at the Zurich main station. And nice hotels within easy walking distance of the station in Luzern. This will save you one change of hotels and allow you to start out right near the Alps your first day. Stay 2 or 3 nights before heading to Wengen (up to you).

For a full day in Luzern, you and your son would enjoy the Rigi round-trip by boat to Vitznau, cogwheel train to the summit (great place for views and walking), train back down to Rigi Kaltbad (more walk/hiking opportunities), and cablecar ride down to Weggis, where you can catch another boat back to Luzern.

https://www.rigi.ch/en

All of this would be included for free if you get a Swiss Pass for yourself, and a free Family Card for your son, which will give him free rides on all sorts of transport when he travels with you (including the high mountain lifts where you only get a discount with the pass).

To cover all your travel, including most of the way to Annency and back to Zurich (via Geneva), you would need either a 15-day Swiss Pass (for 15 consecutive days), or an 8-day Flex Pass (for 8 days of your choice during your travel period).

https://www.sbb.ch/en/leisure-holidays/inspiration/international-guests/swiss-travel-pass.html

Here is a map of the validity of the Swiss Pass (full coverage and discounted coverage):

https://cdn-doc.myswissalps.com/docs/default-source/rail-network-maps/swisstravelpass.pdf?sfvrsn=7788603a_56

How early is your flight home? We always spend our last night in Luzern and just go directly to the airport.

So much to do around Luzern. As someone suggested, Mount Rigi is a great excursion. Check these daytrips out too:

Stoos (cool funicular and amazing hiking)
https://stoos-muotatal.ch/en/train/stoos-railways/

Stanserhorn (very cool cable car):
https://www.stanserhorn.ch/

Pilatus (lots to do for kids):
https://www.pilatus.ch/

Not sure if there is a benefit to renting a car. The trains are great and probably less hassle

Plan 1 that is if you want to spend a night in Zurich. We have always enjoyed Zurich for just a night.

JR - I agree. People here diss Zurich and want to rush into the mountains, which I understand, but I think Zurich is a lovely city and like to spend time there. Especially at Christmas when the markets are open

You’ll find I am the minority here. Everyone but us it seems adores Lucerne. We did not, we actually liked Zurich better. If it were me I would do Zurich first night, then spend 6 nights in Wengen and then on to Annecy. If he’s a nature kiddo and loves the outdoors the more time you can spend in Wengen and the BO the better.

Re: Zurich vs Luzern:

My suggestion (above) was to head straight to Luzern upon arrival, to save a hotel change. Then spend the night in Zurich before their flight home, traveling there from Annency. That way they can have both. 😏

Karl loves Wengen and has been going there his whole life, check out his vlog

https://www.youtube.com/watch?v=qwICuDf0TwY

General recommendation in Europe - train don't car

Thank you. I am so grateful for everyone's support. This feels like, "once in a lifetime" trips so I appreciate all the help.

Questions:
1. Should we abandon the Annecy/Taillores region given transit from Wengen? If so, what other area would you recommend knowing we fly out of Zurich. We have a friend that has a vacation home in Talloires, another friend who has spent weeks there as her favorite place in France. That said, maybe skip?

Rental vs Train given timetable below.

Wengen to Talloires.

Drive: 4 hr
Train/Bus: 7 hr

Wengen to Annecy:
Drive: 3hr 50 min
Train/Bus: 6hr 15min

1. Given transit times would you stay in Annecy instead:

2. Would you suggest swiss rail plus the jungfrau pass? We need to get from Zurich to Lucerne, Lucerne to Wengen, then daily transits using Gondolas etc up and down the mountains to hike, then Wengen to Interlakken or Bern for rental car unless we take the train all the way, then want take train from Geneva back to Zurich.

We were going to get an apartment in Wengen so we can get some meals there, do laundry. We could not find a place down in the Lauderbrunnen valley.

Current plan:
Lucerne 2 nights
Wengen Bella Vista-5 nights
Talloires 3 nights
Zurich 1 night

Thanks again!
Michelle