a layer of flannel works ok for a batting- pre-wash it- the only (down side?) might be you will have very flat quilts instead of fluffy quilts- flannels works fine- is easy enough to work with- and can make the job go quite quickly-
i've done both- used flannel and used regular battings- the flannel batt(ed) quilts are heavier - weight wise- but as i said they are flat- so ---it's a personal choice= if you have access to alot of flannel and it's cost effective for you there is no real reason to not do it that way. just be sure to pre-wash your flannels---they do tend to shrink more than regular cottons because they are a looser weave.