We just returned from 21 days in Poland, with 5 in Krakow. We have done just about everything in Krakow on our previous five trips. My must sees are: Schindler's Enamel Factory, Wawel, St. Mary's, Cloth Hall, the Krakow Underground Museum, the Czartoryski Museum (Lady with Ermine and some Hussar wings!), The Cloth Hall Museum on the second floor, and the Jagiellonian University. Auschwitz really does take a full day and would be on a subsequent trip unless you really want WWII history and the Holocaust.
Don't forget to visit a milk bar. Google for the options. My favorite is Pod Temida.