I use flannel backing on 99% of the quilts I make. My family loves the soft and cuddly warmth you get with flannel. The few quilts I made with 100% cotton are seldom used. So far, the quilts with flannel backing have held up well to repeated washing and drying with very little pilling.
We have 4 cats in our home and cat fur and lint is a fact of life here. LOL!! I recently made my DGD a quilt with Kona cotton in red. The red cotton picked up more cat fur than the flannel.