I use flannel alot!
And, I don't even have a fancy shmancy quilting machine to get the job done. They quilt up great.
of course, I am not making a quilt art quilt, so the quilting is very large and loose.
However! If you choose to handquilt, I don't know if the flannel is as easy to quilt through, which might make a difference for you.
Tip: If you are using pieces for your batting, straighten the edges, butt them up against each other, and rather than zigzagging them together, use lightweight fusible webbing to hold them together - - you will get a flatter joint and more stable also. I usually cut my fusible into 1 inch widths to accomplish the task <wave>