I have used flannel a lot, for my own and families quilts I always back them in flannel and baby quilts are always in cosy flannel. My favourite make is Northcott, especially for babies as their choice of design and quality is so good, this is one I have just finished.
I must confess to never pre-washing my batting or fabrics, cotton or flannel, and the ones that my Sister has, which are dozens, have been washed so many times and with no problems at all.