I'm a bit of a 100% cotton snob. Just from personal experience, I don't mix cotton and poly. My wedding quilts from 1984 have seams that the poly thread cut through. If you've ever hemmed a pair of polyester dress pants with cotton thread, you'll have to re-do it in about 4 months, because the poly wears away the cotton. After about 5 years of wear, my husbands poly/cotton under shirts will just have a mesh of poly, because the cotton gets rubbed away. I did use a poly/cotton for one of my son's baby quilts, and it really wore out unevenly. The poly/cotton was very thread-bare after about 3 years.
So, if you're making a quilt that will last a couple years, or go on a wall, then it won't matter. If you want the quilt to be an heirloom, only use 100% cotton fabric and thread.