I have made MANY flannel quilts. I never buy flannel anywhere BUT a quilt store, and even then I give it a good "caress" to make sure it's thick and well made. I've even walked away from some very pretty flannels I've "felt" in quilt stores. I want something that's going to survive many washings and it won't hold up well IMO if it has that cheese cloth feel. On all my family "snuggle" quilts I put flannel backing on, and my hub's quilt is flannel top and backing.
I prewash the flannels just like other fabrics and then iron them. Some tends to have a lot of shrinkage, and some doesn't. So.. I'd rather get that out of the way PRIOR to making a quilt. It IS personal preference, but what I get out of my lint sleeve in the dryer does not belong in my machine....lol Flannel can be cranky and some has a tendency to stretch. So.. a walking foot is your best friend when making a flannel quilt. Not sewing the top, but constructing the final product.
Several years ago I walked into a LQS and on their 50% off rack I saw a 1/2 bolt of very bizarre flannel. It was taupe with a black wavy grid on it. I would imagine it made some people visually nuts using it, but my family is HEAVY on the testosterone side.. I have ALL grandsons .... and I knew it would be great for guy quilts. When I felt that flannel I was surprised at how THICK it was! I bought the remainder of the bolt, and it has been on the back of 3 quilts and used as a binding on my hubby's project. My hubby's 100% flannel quilt is 5 years old this winter. He uses it every night watching TV because he gets cold easy, and it hits the washer every few months. When I bound it with the same flannel as the backing I sewed it to the back, and machine stitched it down on the front as I knew this quilt would be used hard. That quilt is still in gorgeous shape today! I owe this to having found HEAVY well made flannel.
Good luck...and if you're really not sure make a couple smaller projects and get the feel for how flannel behaves. Also, when sewing with flannel I don't pick out a real intricate pattern. If you get to making something with a big center seam intersection like a star I think the thickness of the flannel would make that a PITB to deal with....LOL