I use flannel as a backing all the time and I leave out the batting if it's a kid's quilt that is intended to be carried around a lot. If I want it fluffier, I use batting. If you pin and quilt it together in sections, you shouldn't have a problem with puckering.
I also do fleece and flannel quilts which don't need batting. Here's the posting
http://www.quiltingboard.com/t-52843-1.htm.
I've never done cotton with fleece but I'm sure it can be done with no problem.