Staying in Ceske Budejovice instead of Cesky Krumlov.

Budejovice is an agreeable enough city to spend one or two nights. I had it as a stop between Austria (Linz) and Plzen (Pilsen). I can't judge whether it's preferable above staying in Cesky Krumlov itself, but it has no tourist crowds and it's only a short train journey of 30 to 45 minutes (use the CD site for the train planner).
Hotel Zvon has a marvellous location on the central square.

Added:
The CD site only shows trains operated by the national railways CD. The European train planner of the Bahn also shows the trains operated by the regional railway company.

While this is certainly possible I would recommend to stay overnight in Cesky Krumlov. Day trippers disappear and night C.K. has its magic. C.B. is a regional city, quite bigger than C.K. C.B. downtown is pretty and historical albeit not as C.K. If you stay in Ceske Budejovice you can do an original Budweiser brewery tour. Their beer tastes much better than St.Louis Budweiser. There have been many lawsuits (you can learn more about it in the brewery) about this trademark. I think Ceske Budejovice will probably ultimately win. German name for Ceske Budejovice is Budweis. But on the other hand St.Louis Budweiser has more money.

I did that once years ago, as suggested by Lonely Planet, but after visiting Krumlov, I realized that they had it backward. I usually prefer staying in the smaller, cuter spot, as well as it's good to be there after the day trippers leave.