I have done both tours, first My Way and then Switzerland, because My Way was introduced first. I enjoyed them both. I am glad I experienced what I did on the Switzerland tour as it has helped inform what I want to visit again. Switzerland is a well-rounded intro to the various areas of the country. And, sleeping in Mürren is pretty fantastic.
However, My Way is for me a tour I would consider repeating. I don't have to return to Lausanne and probably not to Lugano, and not to Zermatt. They were great, but, for me, the Dolomites, Bavaria, and Salzburg are all places I have visited more than once and plan to visit again. While both of these tours have equipped me to undertake the alpine area on my own, I like the support structure and yet the personal freedom of My Way.
Note, if you do visit the Alps around this time of year, give a look out for cow parades (Almabtrieb, Alpabzug, Alpabfahrt). I was able to join in one outside of Innsbruck one September. Google this topic if interested.
Not sure I have been helpful... Oh, and my time in Füssen was fun, relaxing, and vacation-like. One of those times and places I took a vacation from my vacation, as RS sometime says. I joined tour mates in a visit to Hohenschwangau and lunched on boar-burgers at the local lake. I dined at a fantastic Greek restaurant in an old fortress and listened to a concert in the townhall's courtyard. Füssen was the point of the My Way tour when I actually ditched my to-do list and kicked back. I needed that.
Good Luck in your decision. I may put myself on a waitlist for My Way, but I am taking travel decisions easy just now. Oh, and did I mention the cost difference? Nothing to sneeze at.