I love using flannel as a batting!!
Pro's ...
it's sooooo soft and supple. The drape is better than any batting you will use. You can easily wrap it around a baby's finger without folds or stiffness.
Very warm, but still breathes
You can quilt is far apart if you wish since the batting is a weave.
Cons ...
It doesn't show the quilting as much (this may be a pro <g>)
can be a little on the heavy side
Washes beautifully (I don't care for the crinkly look ... this may be a con!)
Highly suggest washing the flannel at least twice in HOT water and a HOT dryer to make sure it shrinks properly.