I used flannelette for a batting several years ago. Washed/dried on hot/hot several times to get the shrinkage under control before taking all to some Amish ladies to handquilt.
They liked working with it. It has not had any further shrinkage with washings and I have not seen any crinkly-ness or wrinkles show up. I really like the feel of it ... nice body, not stiff, and quite comfy when used on the bed. In the summer, just a sheet and this quilt. Wintertime, add on an extra quilt(s) for more warmth.
While many say flannelette is heavy .... combining this one layer with traditional quilting cottons for the top/bottom has not made for a heavy quilt to move around. I actually find it quite light.
The quilting does show, but no you are not going to get a poofy look, being that there is no loft in it. If you want the quilting more noticeable, try a thread with more contrast and perhaps a heavier weight.
All in all ... I've had no regret in using the flannelette as a batting.