Your trip looks good to me. I had 10 nights, and spent 3 in Luzern, 4 in Mürren, and 3 in Lausanne (flying into Zurich and out of Geneva, but not spending any nights in these cities). It was a wonderful trip, so I think yours will be even better (more time is always good).
The Jungfraujoch and the Schilthorn are two very different experiences. With 4-5 nights in Mürren, there's no reason you can't do both; just make sure the weather is good before you spend the time and money for each (there are webcams you can check - ask at your hotel's front desk). From the Schilthornbahn, you have views across the valley to the mountains; at the Jungfraujoch, you are in a "saddle" between two mountains. Both were great for me.
I wasn't taken with Lausanne, although I loved the Museum of Outsider Art and liked the Olympic Museum. My stay there was fine, but also look into Vevey or Montreux. From any of these, you can easily visit the others.
I was there in 2014, and at that time, a 15 day Swiss Pass was the best deal for me. However, the terms have changed since then; you'll have to crunch some numbers yourself. One thing to remember is that with a Swiss Pass, you only have to buy tickets for things not fully covered (such as the Schilthornbahn, the Allmendhubel, and the Jungfrauhoch). For everything else, you just get on, and flash your pass when tickets are checked. This is a great convenience, particularly in the Berner Oberland, where you're always riding on something. The Swiss Pass (at least in 2014) also included museums, which helped me make it pay off.
On the other hand, the Half Fare Card can also be a good deal. It gets you 50% off of anything that moves in the entire country, including the Jungfraujoch (only 25% off with the Swiss Pass). It costs 120 CHF, so if you're taking more than 240 CHF of rides (and in two weeks, that's almost a certainty), you can't lose. You do have to buy tickets every time. But, even the ticket machines for local buses have the half-fare option.
I saw Mt. Rigi rather than Mt. Pilatus, for the simple reason that the trip to Mt. Rigi was completely covered by the Swiss Pass, while part of the trip to Mt. Pilatus was only 50% off. For Mt. Rigi, you take a boat from downtown Luzern to Vitznau, a train up to Rigi Kulm, a train down to Rigi Kaltbad, then a cable care down to Weggis, then a VERY STEEP walk down to Weggis dock for the boat back to Luzern. This was a very full and enjoyable excursion, taking most of a day. If you don't want that very steep walk down, take the boat both ways to Vitznau, where it is a short and only slightly inclined walk between the train station and the dock.
I hope you have Rick Steves Switzerland - he has lots of details on the places you plan to see, including all the logistics.
