We have two weeks, what are the recommended sites to see? Are there other cities recommended to stay in on our loop?
The answer to your first question (and probably your second question!) lies in the 1400-page Rick Steves Eastern European guide; it provides a good overview of the recommended sites to see for all the cities you have listed and their surrounding areas.
I know you can find this info in Rick Steve's book, but I was hoping to get input from others who have taken this loop or a portion of the loop, to help narrow down some of the places to see.
As an aside, I definitely don't think you want to do overnight stops in more than 4 cities in 2 weeks (though day trips out from the cities where you are staying are certainly reasonable). Do a little research; put together a sample itinerary; post it along with info on who is traveling, their ages, and their interests. Then, the board can be much more helpful to you.
Would it be a terrible problem to skip one destination? Of your two weeks the best of 4 days are spend on getting from one destination to the other, leaving you 10 days to do what you want to do. A more relaxed and rewarding trip would be: Kraków - Olomouc - Prague - Ceske Budejovice - Vienna - Brno - Kraków. Some places can be a one-night stop; others for two or more nights.
It wouldn't be terrible, but I have a bucket list of at least 10 international trips I want to take and I can't afford and or there are places I want to see yet in the US as long as I am still on this earth. So with approaching 63 I want to see as much as I can when I am in an area. I hope that helps.
Dave ask that I put in some of the things I want to see on my trips between the cities, so far I have Auschwitz, Cesky Krumlov, Danube Valley and things in Slovakia. What over things should I see? What is the difference between the Danube Valley vs the Danube Bend?
Danube valley is in Austria. Danube bend is in Hungary. More about it on google.
I want to see as much as I can
My point was (and is) that there are so many worthwhile things to see and enjoy outside the capitals.
I would skip CK, not the least interested in the place. Given your itinerary so far, I can put together one especially if you are deeply into the history.