As David S. mentioned, maybe we should do:
Land at Frankfurt (recover for 1 night) --> Wurzburg (1 night and start romantic road driving with 2 nights on the road) --> Fussen (end of romantic road, return rental car and train to Switzerland) ---> Murren (3 nights) ---> Lucerne (1 night) --> Bern ( 2 nights) ---> Munich (3 nights and fly back home)
Seems geographically this makes more sense. Is it?
I don't know where you can return your rental car but probably not Füssen. And even if you could getting to Switzerland from there with public transport is going to be slow. I assume from this alternative itinerary that your flights are already fixed.
If they are I suggest you evaluate the cost of keeping the car until you get to Munich. Making the trip to Füssen -> Switzerland -> Munich is going to be faster with a car. It is going to be dead weight while you stay at Mürren but it might be worth considering. Some comparisons: Füssen -> Lucerne is 3.5 hours by car vs 7 hours by train and Lucerne -> Munich is 4h by car vs 5h by train. So a complete round trip is 7.5h vs 12h.
If they aren't. have you considered flying out of Zürich and sandwiching Munich between Füssen and Switzerland? I'm sure you could return your car in Munich and you'd have a choice between decend public transport connections or even a flight to Switzerland.
We are not planning to drive in Switzerland. Should we?
Your routes between Füssen/Munich and Mürren/Lucerne doesn't really put you on the track of many scenic driving routes (that I know of). One option would be to make a slight (1.5h) detour over the Kausen pass between lake Walensee and lake Lucerne. That's a nice, slightly adventerous drive. Another option is what I did with my GF when returning from Munich: Through Austria. Most of the drive wasn't particularly noteworthy (Autobahn) but we did have some nice parts on local roads when going over a pass (can't remember which though). We did however go through Garmisch-Partenkirchen to see the Partnachklamm which put us on a slightly different route in the beginning. Personally I wouldn't make that detour for the road but the Partnachklamm was sweet.
Finally, I also would rather put one of the "Berne nights" towards Munich, Mürren or possibly even Lucerne - Unless you have something specific you want to do there that necessitates another night.
I wonder if we will miss something without stopping at any major city in Switzerland ?
From what I've read on blogs most Americans don't consider Switzerland to have anything that would qualify as a "major city". So barring that what are you looking to see? Personally I don't really care much for the cultural side of cities. I instead appreciate distinct looking cities and towns. On that note I think Berne and Lucerne qualify as worth visiting. Google the sights of both and see if anything grabs your interest enough to warrant putting in a day there over somewhere else.
You could even drop Berne entirely and add another day in Mürren to saveguard against bad whether. You can easily do Berne or Thun as a day trip from Mürren.