There is one situation where I definitely prefer cotton thread , and that is when working with gingham. Now that's odd, isn't it? Because gingham is a poly/cotton blend.
The reason is that gingham is a very lightweight fabric, and the stitching lines tend to pucker when I use polyester thread. If I use cotton thread, the stitching lies flatter. I have thought and thought about it, and I believe it is because the polyester thread has a bit of stretch to it, while the cotton thread has almost none.