I made a quilt with a flannel back for my husband because I knew he'd like the softness and extra warmth. As others have mentioned, the quality of the flannel is important. Mine hasn't pilled yet, but I don't wash it often. Lint has not been a problem either.
It was a little harder to work with, because it's more stretchy, or maybe I didn't smooth it out well when I was making my sandwich. When I was quilting it (stitch in the ditch) it would sometimes fold over when crossing another seam line, and I wouldn't realize this until I was done with the seam and then had to redo it. I learned that I had to hold the quilt a little taut while I sewed.
I prefer regular cotton fabric backing for myself. I don't mind flannel shirts, but for some reason I don't like to have flannel sheets/blankets touching me.