For Munich:
Visit to one of the lakes like Starnberger See or/and Chiemsee is also a nice todo for the kids. Rent a boat or just take a swim.
Visit of Schloss Neuschwanenstein. (Castle) in Füssen.
https://goo.gl/maps/Tnq7PWKgrUtSbJdE6
(Could be very crowded, with hours of waiting time to get in.)
For Stuttgart:
Visit to the Mercedes Museum. It's huge, plan 3-4 hours at least!
The old Towns of Ulm and Nuernberg have some nice spots as well (I don't know where you plan to go from Munich to Stuttgart.)
However they where bombed havely in WW2 and many of the old town buildings are gone. (but same in Munich and Stuttgart)