We have driven from uk to eastern europe several times with small children. This last year we stopped in nuremburg. We stayed at a hotel that was fab for them- they were given playmobil gifts on arrival, a playroom, swimming pool, sand area to play in. There is a playmobil fun park in the area, and nuremburg has an amazing toy museum as well as being a lovely but not too big place to visit.
We've loved Austria, particularly Vienna, Mondsee, Salzburg.
One of our faves is Budapest, as it is relatively cheap, but enjoyable with most of the baths and museums being fairly child friendly.
There are so many nice places off the beaten path and places we have stayed when got lost because they were too nice ......
Have a lovely time wherever you land....