I have not had problems with too much unraveling, but I have only used flannel a few times with baby quilts. It is a little fuzzy and a good bobbin cleaning is needed after, but I love it and it gives the quilts such a snuggly feel. I do think flannel requires really good basting, but then again, what project doesn't? I say go for it and let us see a picture of the result!
PS I prewash my flannel too, but did not prewash the top fabrics on my last baby quilt, which I am working on now. We will see if that proves to be a problem!