I think that Mountain Mist Lite batting (it is polyester) would be good since you will be quilting instead of tying. It is very thin, adds very little warmth, but provides a little puffiness. Requires quilting lines no more than 3" apart. I have used this batting for baby quilts and it quilts up very nicely. The quilt remains very soft too. Our local JoAnne Fabrics carries it, and it is inexpensive.
If you can spray baste with 505, that is one of the best ways to prevent stretching of the minky.
Also, I ***strongly*** recommend heavily starching the flannel top before layering. I recommend a 1:1 solution of Sta-Flo liquid laundry starch and water. The way I do it is very easy. I use a large wall painting brush to saturate the fabric with the solution (kitchen island works great), wait a minute or so to make sure that the starch has a chance to penetrate the fibers, toss in the dryer, then iron with steam. This heavy starching ensures that the flannel will not stretch or distort on you while machine quilting. To get rid of it, just wash the quilt once after it is bound.