I prefer cotton batting. But I also think most of the brand name battings will hold up nicely to daily use. Be sure to think about shrinkage especially with flannel. If you like the crinkly look, you don't need to prewash as both your flannel and cotton or wool batting will shrink 3-5%. If you don't, be sure to prewash both your flannel and batting. The only batting that doesn't shrink much is poly in my experience.