Your problem is too many great options! haha!
We are doing all the spots you mentioned, but it will have taken us two 2wk trips to do it. Our first trip we did: Munich, Passau, Vienna (stop in Melk), Salzburg (with day trips to lake and mountains including Hallstat), Garmisch, Legoland, then back to Munich. This trip we are doing Frankfurt, Bamberg area (including Regensburg, Nurerberg, Rothenburg), Prague, Dresden and Berlin.
Salzburg was lovely, but we only spent a day and a half touring because it was so touristy and so busy. The rest of our time in that area was spent going to Hallstat, Jenner Mountain, Konigsee and the lake region (In a circular route, stop in Strobl, St. Wolfgang, Bad Ischl, Ebensee, and Gmunden before returning to Salzburg.)
Garmisch area we really didn't do much in Garmisch itself. We used it more for a hub for day trips. We had a car, so not sure how feasible it is for you to do by train. From Garmisch we did: Neuschwanstein & Hohenschwangau, Liderhof, Mittenwald, Oberammergau, Ettal.
The thing is, no matter where you choose to go, if you do a little research, you will have a wonderful time. There is so much to see and do, you can't really make a bad choice.
We really enjoyed our time in Munich. I wouldn't hesitate to spend the 4 nights there. There is so much to see and do. The Deutsches Museum alone can take a full day...and is worth it.
Oh and I wanted to add....sometimes the most touristy thing can give you the best memory. Back in 2012, my youngest was only 9 when we took the kids to Germany for the first time. In Salzburg, right in the middle of the crowds, there is a giant chess board. My oldest (who was 14 at the time) and my youngest were playing a game of chess. Two local old men (who spoke no English) were sitting on a bench nearby. They began coaching my youngest. He made the final move (at their direction) to win the game. The old men cheered. My kiddo went over, shook hands with the men, got a grandfatherly pat on the back. It was the most precious thing. To this day, he will tell you that was his favorite memory of our entire trip.....even better than Legoland.
Have fun!!!