Help picking cities / sights for family (tween ages, 11 and 13). Starting in Munich

One thing I would recommend would be a Sommerrodelbahn -- they come in slide and coaster variants. Super fun, especially at that age. You should be able to find them easily enough regardless of your route.

Can you give us any other interests? Length of itinerary?

Themeparks such as Legoland in Bavaria or Europa-Park in Rust (not far from Basel) can be fun for the kids.
Some other ideas for destinations with kids in Bavaria.

For the German part: on this map you can discover possible destinations based on your interests.

I think Salzburg is a great place for kids (and is close to Munich). An enormous medieval fortress rests above the city and is waiting to be explored. There is a palace just outside of town with trick fountains. Mirabell Gardens is a gorgeous royal garden with a smaller Dwarf Garden with small statues dating back as far as 1715 (see the Atlas Obscura article). Nearby Berchtesgaden offers great outdoor activities. The best of those, to me, is Königssee. Take an electric boat across the lake, get off at the Salet stop, take the 15-minutes walk to Obersee, admire the Instagram-perfect view (go early to avoid having Instagrammers cluttering the view!), hike around the left-side of the lake, admire the view from the opposite side of the lake, ascend toward Röthbach Wasserfall (the tallest waterfall in Germany) to find a gorgeous alpine meadow surrounded by granite peaks, and then continue on to the foot of the waterfall to feel the cool breeze coming off the water. Watch your step! Cows graze here during summer. Head back the way you come and stop at the snack shack on Obersee -- you can sample fresh-collected raw milk from the cows or get more traditional snack shack fare.

Things to do with kids in Salzburg: https://roamaustria.com/salzburg-with-kids/

Oh, and the salt mine tours are super fun! I think I was about 11 the first time I did it.