Assuming you’ll be there in summer, I really liked the Oetz Valley in Austria. It’s a ski area in winter, but a really pleasant valley in summer, with lift-accessed walks in Alpine scenery. Easy access from Oetztal train station by bus (not included in the pass, but there is a deal with many accommodation providers to give you free transport in the valley + other discounts via the Oetztal Card).
Innsbruck is a nice compact city, if you want to spend a few hours or half a day between trains. It’s more compact than Salzburg, for example.
A third place worth a stop is Kuftstein, very pretty. Two hours between trains should give you a chance to have a look around the town. If you visit the tourist office in the main square, they have a free map to a walking tour around the town - that will take around an hour.
All those are on the logical route from Munich - Austria - Switzerland.