5-6 Days in Germany with kids, train in June

How about a stay in Nuremberg, with outings to the smaller villages you mention?

Nuremberg is in northern Bavaria, with direct access to FRA airport after a2-hour train ride. The oldtown zone is largely pedestrianized andcharming and makes for interesting walks. Nuremberg has its own castle and LOTS of museum options:

Imperial Castle: https://tourismus.nuernberg.de/en/discover/places-of-interest/location/imperial-castle/

A few of the many museum options:

https://tourismus.nuernberg.de/en/discover/museums/family-childrens-museums/

https://tourismus.nuernberg.de/en/discover/museums/location/db-railway-nuernberg-db-railway-museum/

https://tourismus.nuernberg.de/en/discover/places-of-interest/location/germanisches-nationalmuseum/

https://tourismus.nuernberg.de/en/discover/museums/unusual-museums/

https://tourismus.nuernberg.de/en/discover/museums/science-technology-museums/

The Craftsmen's Courtyard: https://www.youtube.com/watch?v=mU7qmhO5uwM

Zoo: https://tourismus.nuernberg.de/en/discover/places-of-interest/location/tiergarten-nuernberg-zoological-garden/

Near Nuremberg and accessible on a short outing by train:

The Franconian Open-land Museum in Bad Windsheim, a cultural center of sorts with a collection of historic buildings where the past comes alive.

Iphofen (old-world wine/artists village)

Bamberg (UNESCO World heritage old-town center)

I would do Salzburg. Salt mine for sure, Sound of Music tour ( re-watch movie to refresh your memory. Many of the sights in the old town which is pedestrian only are not visited by the bus tours ). Perhaps the ice cave at Werfen.

Rothenburg

Those two would be good for your 5-6 days

Since you might drive by, Weissenburg in Bavaria is a really nice town worth stopping for a quick break. Fairly Medieval with city walls now a leisure area.

..and again the Altmühl Valley from me :o)

Small Villages Castles,Falconary, a cave, Boatrips, Crystalmuseum Bavarian style food

Small Villages: Kelheim, Essing, Riedenburg and more

Castles:Burg Randeck Burg Prunn and Schloss Rosenburg (Falconary)

Boatrips on Danube to Weltenburg Monastery and on the Altmühl/Main Donau Canal

Small Crystalmuseum in Riedenburg

Icecream by the Riverside in Riedenburg

Good local restaurant in Essing Riedenburg and Kelheim

The Schulerloch Cave

The Befreiungshalle (Liberation Hall) above Kelheim Go there by small roadtrain from the Danube Riversside (Carpark Wöhrdplatz) near Kelheim

and more ...

Summary on Family Adventure Riedenburg

Accomodation for some days
in at Landhotel Schneider in a small village near Riedenburg
or Farmstay at Ferienhof Halbig near Riedenburg

But you ll better do that by car

By car
3hrs north of Salzburg via Munich
1 hr south of Nuremberg and 2hrs of Rothenburg ob der Tauber

And another option:

You could go to Lake Constanz, where you have Lindau, Meersburg, Mainau, ferry rides, Zeppelin rides, etc. Very easy to get from there to Frankfurt (straight north). And if the kids (or you) have any interest in cars you have both the Porsche and MBZ museums in Stuttgart on the way.

Also several good places to stop if interest is in dinosaurs/paleontology.