I like cotton thread. It feels and handles well and as I hand quilt that is important.
I decided to do a small place mat sized quilt for my daughter in laws wheel chair table, and thought I would try my hand at machine quilting it. Since it wasn't intended to be heirloom I used some polyester thread I had accidentally purchased. I hated it. It was so crawly I found myself wanting to scream before I finished that project. When it was done, I threw the remainder of the spool in the trash.
I remember once seeing a bumper sticker on a Ford that said "Friends don't let friends drive Chevy's". To each his own. In other words, if it works for you, keep doing it.