First pilling - It's impossible to know if a flannel is going to pill or not. It happens more often with cheap fabrics, but it also happens with quilt shop fabrics. I just use flannel on really fluffy quilts that won't be washed often.
Second: prewashing flannel - I choose not to. However, if you are combining very light fabrics with dark fabrics, you have to or the light fabrics will become dyed. I put the darks into cool water on gentle cycle (shortest cycle). I do a double rinse. Then into the dryer. I have not found hot water to be helpful. It doesn't release or set dye any better than cool water. If this is to be a showpiece, then you might consider a second soak without agitation to be sure that it has released all of its dye. The light fabrics don't usually release dye - just short cycle and dry. I found it helpful to use starch when working with prewashed flannel.