On one vacation I spent 4 days each in Prague-Krakow-Berlin with a train ride day in between. Saw them in a row.
If someone could only see one of those three and never see the others, I have one recommendation and the choice is not even close.
The only pick for #1 is: Krakow. ^ ^ ^ ^ ^
Once you feel the vibes (its the Chakra point, don't cha know?) you will understand. Just don't tell everyone, we don't want it as overrun with tourists like Prague.