ljonespranis, I would be doing you a huge disservice if I started making comparisons between two cities or trying to sell you on one, when I have only been to the other. If I were to let my personal bias kick in, I would say leave Krakow and follow this route: https://maps.app.goo.gl/owheLGcMSdMSqrEy5 But thats not the question you asked so ............ LOL
Back on topic, I know my teenage kids (2 boys and a young lady) got a kick out of the underground stuff in Brno (bunker, labyrinth, bones). Its one of the more lovely small cities I visited in Central Europe. But I presume there are others equal or better.
For any place I might be staying or passing through I always go to VIator and GetYourGuide; not to book, but to see what people want to see in the area the local tours and the day trips. In a lot of ways better sourcing of information than articles.
EDIT: The night train is a good experience for the kids, and something I did once by choice and then twice more because there were no options. Speaking of that, If you really want to give the kids a great night train experience then take the bus from Krakow to Lviv, spend a night or two, then book the night train to Prague (RegioJet). The family will never forget it (mostly in a good way). For some unexplained reason I had Bpest on the brain, should have said Prague.
Okay, I will get serious again, The trip from Krakow to Prague can be direct and quick (night train or a flight) or it can be a journey with a night or two along the way (my vote). With some investigation you can probably do the trip with a couple of stops using nothing (or mostly) a train.
I envy such problems in life.