12 days in Switzerland...pl help me

Ummm, how old is your son? If he is young enough to enjoy some of the specifically children's things, I doubt if he would appreciate the castle (NOT 'palace') at Chillon.

I think that Mount Pilatus and Mount Titlis would each require more than half a day: after doing one, you might not feel any need for the other.

The 'Golden Pass' route is gorgeous, but combining it with a tour of Geneva in just one day sounds like quite a lot.

I found both Interlaken and Zermatt rather boring in themselves, although they give access to good mountain areas.

Everything is doable. But it will not be a trip for people travelling on a budget.
Some fares:
Lucerne - Titlis and back: 130 USD
Luzern - Pilatus and back: 105 USD
Interlaken - Jungfraujoch and back: 205 USD
Interlaken - Schilthorn and back: 135 USD
Zermatt - Gornergrat and back: 90 USD
Zermatt - Kleinmatterhorn and back: 100 USD
You can get some discounts with the Swiss Pass and with the Swiss Half Fare Card:
http://www.swisstravelsystem.ch/en/content/offer/tickets/
http://www.swisstravelsystem.ch/fileadmin/pdf/STS-GB-M-11-EN-WEB.pdf

You plan to visit 3 Swiss towns. Lucerne, Geneva and Zurich (the other places you mention are holiday resorts with no historic buidlings, museums, etc, except Chillon castle). I suppose you know that there are more interesting towns in Switzerland than these 3.

Now to your questions:
Pilatus in half a day is possible. My sugestion:
Leave Lucerne city center by bus at 8.15, change at Kriens to the cableway and arrive at Pilatus at 9.21. Enjoy the panorama. Leave Pilatus at 10.50 by cog railway up to Alpnachstad, change there to the Lake Lucerne boat and arrive at Lucerne at 13.11. You may leave the boat 10 minutes earlier at the Transport museum pier and visit the Transport Museum in the afternoon.

Which Lake Brienz Dinner cruise? 1 boat leaves Interlaken at 16.25 and comes back at 18.50 (wekends from mid June, daily in July and August), another one cruises between 19.00 and 21.15 (saturdays from July 9th to August 21st only).

Harder is close to Interlaken: 10 min by cablecar.

The Trummelbach Falls are of easy reach from Lauterbrunnen, between Interlaken and Jungfraujoch.

Chillon castle is a 5 minutes train, boat or citybus ride from Montreux. There is also a promenade (nice walk) along the shore of Lake Geneva.

Geneva has some good museums. If you don't get lost there, you can easily visit the town in one day. You don't need any guide.
You could also go back to Montreux by boat:
Geneva Eaux Vives dp 15.00 - Montreux ar 19.23, or
Geneva dp by train 17.36 up to Nyon, then boat Nyon dp 18.27 - Lausanne ar 20.20. Lausanne - Montreux by train (20 minutes, 3 trains every hour until midnight).

The chocolate train excursion to Gruyeres and Broc takes the whole day. Chillon castle would be closed when you come back to Montreux.

Zermatt: Gornergrat is as good as Kleinmatterhorn. But it's not forbidden to do both (if the weather is fine, otherwise it wouldn't be worth the money).

Zermatt - Rheinfall: take any train leaving Zermatt between 7.39 and 18.39 (departures every hour), change at Visp and Winterthur; 4 1/2 hrs later you will arrive at Neuhausen am Rheinfall.

Swiss timetable: http://www.sbb.ch/en/index.htm

Thanks a lot. Opened my eyes fully. My son is 10 year old...not sure if he is going to enjoy the views. He is keen on toboganning, husky rides and playing with snow. Would I be able to do so at one of these excursions at Titlis or Pilatus. I am confused between doing Pilatus or Schilthorn and Gorgengrat vs Matterhorn. Maybe if I choose one each from the set, maybe I will be able to reduce my days and cost :). Also looks like i should give Geneva a miss. Have kept the 3 towns as a base so that travel is easier due to the kid and luggage. Do let me know options that could bring down my hotel rates and would be accessible to places. Many thanks once again...wondering if I need to go back to the drawing board to chart the routes again.

Snow: you never told us in which month you plan to travel. Euope has 4 different seasons: much snow in January and almost no snow in August (only at places above 3000metres).

If cost is any kind of issue, then you could economise on hotel rates by renting an apartment for the week and visiting other places as day trips.

That means up to 8 hours in trains per day.

Re reducing hotel costs. I highly recommend the Swiss Hostels especially when traveling with children. It gives them a chance to meet and mingle with other local children, They have family rooms which are quite comfortable, some even serve breakfast and a good fresh dinner. check it out. It was a highlight for my grandson when I did a trip a few years ago.
You can't get better advise then what Neckervd gives. He knows his country well

Thanks for all your advise, am doing the following now with all the inputs, 2 and half days in Zurich...the half day is to free ourselves from the long flight journey. Moving to Interlaken and staying for 6 days in a hotel near Interlaken which I got a real bargain deal on. Moving to Lucerne for 4 days and post that will fly back. We plan to explore the smaller towns around Interlaken and Lucerne. Am still populating that list and will share for advise soon. Neckervd : your inputs were really helpful in building the new itenanary. We are travelling around 19th May and will be there till 2nd June. I am buying the 15 day Swiss Pass, guess that should suffice and will give me great discounts.

"a hotel near Interlaken which I got a real bargain deal on":
That's normal, the hotels there will be almost empty in May.