I have done both. I find the regular cotton is more "user friendly" than flannel when it comes to binding (and turned applique!). If your are out of flannel other than scraps, and I was in your position, I would choose a regular cotton that compliments the quilt from stash and not make a special trip/purchase for more flannel. I have not noticed a difference in wear between flannel and cotton but I have noticed that a bias cut binding wears much better than straight of grain cut binding. Additionally one of my most used quilts I bound in flannel and this quilt is at least 10 years old (probably older) and what I have noticed is the "nap" has worn off the flannel so it has the appearance of a regular quilting cotton now. Finally, if you are doing a standard 1/4" binding so little of the fabric shows most won't even notice that the binding is not made of flannel.