I was going to recommend Krakow, as it's a wonderful city with a great deal to see and explore, but it is a fairly long train ride from Prague. I did the overnight train between the two, but if you don't sleep well on trains, that's not going to be a great option for you.

You may want to look at this site for information on low-cost airlines out of Prague. As you've already noted, there don't appear to be many direct flights available.