I have been told and read in several quilting books that poly, being stronger that cotton, will cut through the cotton fabric after time. So I use cotton for cotton. I wanted some variegated thread one time, and found some beautiful colors at my local quilt fabric shop. I never thought to ask if it was cotton, just assumed it was. When I got it home, I quickly realized the feel was completely different. It felt slick. Checking more closely, found that it was polyester. I still have it but never used it.
For hand quilting, I prefer YLI coated hand quilting cotton.