I have used flannel for batting several times, the 'hand' of the quilt is a bit softer. For Christmas last year I made quilts for the grand kids and ran low on my warm and natural and used flannel for one of the kids. It came out just as good but actually felt a little less heavy.
I now buy solid color flannel with the sole purpose of using it as batting.
Just be sure to prewash it!
warm quilt hugs, sue in CA