Krakow to Prague, stop at Wroclaw or Olomouc??

A few questions:
1) From where are you flying into Berlin? I'm assuming it's from the US, which means jetlag, but please correct me if that's wrong.
2) What overnight train are you taking? I looked on bahn.com on Dec. 4, and found one direct that leaves Berlin at 18:43 and arrives Krakow at 5:29. Is that the train? Because the others I saw leave later but you have to make one or two transfers.

From what it sounds like, you'll arrive in Berlin sometime in the morning/early afternoon on Dec. 4, make your way to the train station, and then board an overnight train. Even if you take the direct train, that means waking up EARLY the next morning. Have you ridden an overnight train before? Have you slept on one? I have, from Berlin to Vienna, and honestly, I slept great. However, the train I was on did not make 17 stops, which yours will. Something to consider.

I'm not saying don't take the train. It will be an adventure! This is just a long way for me to say you are going to be draaaaaaaaaaging on Dec. 5 when you arrive in Krakow. It will likely be a "wasted" day, as far as actual sight-seeing. Lucky for you, though, Wedel (the chocolate store on the main square) opens at 9am, and I consider sitting inside sipping flavored hot chocolate a Can't Miss Activity when you are in Krakow in December. Anyways, that leaves four full days to see Krakow, and Auschwitz will take the better part of one of those, and the salt mines (which are awesome) most of another. Keep in mind it will be cold, and will get dark early.

My point: Stay the full five nights in Krakow. You will be tired after traveling for basically two whole days. Take the extra night to recover from jet-lag and enjoy the city.

It sounds like a great trip! Have fun!

From a practical standpoint, Olomouc will be a much easier stop. Wroclaw is more of a detour than a stop-over. If you took the train directly to Prague, the train would pass through Olomouc anyway. In theory you could stop off for just a few hours to break up the train ride, but I don't recall if there are luggage lockers at the train station or not.

Olomouc is not a particularly lively town (what a contrast to Prague both good and bad). Wroclaw is a more interesting town in my opinion - all else being equal, I'd stop in Wroclaw instead. But all else is not equal - Wroclaw is quite a detour by train between Krakow and Prague. I'd probably choose Olomouc. And I'd want to explore it in the daytime; you will have short days in December, so try to get there early that first day.

A night train with so many stops sounds like a nightmare to me, and I'm still puzzled about why the Deutsche Bahn website doesn't show the sleeping carriages as running all the way from Berlin to Krakow, but that aside:

I visited both Wroclaw and Olomouc during the summer of 2018. Both are fine destinations, but--at least in the summer (when Olomouc isn't full of university students)--there's a huge difference in the atmosphere. If you seek a place that's not as touristy as Krakow and Prague, Olomouc is a wonderful choice. Wroclaw is larger (six times the population of Olomouc), deserving of more time and overrun with dwarf-baggers. There are English-language walking tours offered in Wroclaw ("free" but you need to tip); I found no such offerings in Olomouc.

One other possibly-useful data point is that--although Olomouc isn't particularly large, it's quite a walk from the train station to the core of the historic area--almost 1.5 miles to the astronomical clock.

There are sometimes walking tours available in Olomouc - but not when I was in town (September); there just weren't enough other tourists. I asked! I'm guessing December would be even quieter.

I took the local tram from the train station in Olomouc to the old town so didn't have to walk.