I do applique & have run into problems using WonderUnder with anything other than 100% cotton (I called Pellon & they said it is designed to be used exclusively with 100% cotton). So no more poly or poly-cotton fabrics for me.
And Mdegenhart is right, the cotton will separate from the polyester over time with repeated washing, resulting in pilling. 100% cotton will fade, fray & thin, but you don't get the horrible pilling like a blend. That said, quilt with what you like.
Cotton makes me happy, so I quilt with all cotton fabric, thread & batting.