You should give some thought to how you plan to quilt the finished product, as flannel is, in my opinion, a little harder to quilt. For one thing, it's heavier, so with a large quilt, you will have a lot of weight to manipulate.
Another thing is that it's "stickier" so free motion quilting can be harder, though certainly not impossible. I definitely reach for my gloves and the super slider teflon sheet when I'm quilting flannel.
RST