Polyester thread is shiny and beautiful in a quilt, and yes, many of the quilters today are using it, longarmers are definitely using it. I love it, myself. I think some FMQ quilters are recommending it because of tension problems they've had. I suspect some of those problems would have been rectified with a good needle to thread match and a well-oiled bobbin (so it won't kick back).
In my previous life of quilting (I took a 10 year break) the talk was that you should always use cotton. However, really, there is no need. The idea was that polyester would saw through quilt fabric. However, hand quilting thread is a whole lot stronger than polyester. If polyester would do that, hand quilting thread would too. But it doesn't.
I think you should use whatever you like the best.
I hand quilted a whole cloth wall hanging all in Guterman hand quilting thread (the 10 year old form of it). It was gorgeous. Whole cloth quilting is greatly about creating textures. You can do that with many kinds of thread.
Use what you love (and aren't allergic to). It will all hold up just fine and look gorgeous.