It's true that cotton and polyester fibers break down at different rates and fade at different rates. The fading issue becomes obvious over time in quilts that are made with both cotton and poly fabrics; the cottons fade while the poly's remain vibrant. However, fading will not be an issue if the cotton and polyester threads being used together are white or cream-colored. The breaking down at different rates is probably also not an issue for piecing.
There are a lot of considerations that can be taken into account. I have done piecing with poly in the bobbin and cotton on top. On my machine, however, I noticed that the seams made with this combination did not lie as flat as seams with cotton thread both top and bottom. I noticed the same problem when piecing cotton fabrics with polyester thread both top and bottom. That's why I switched back to cotton thread both top and bottom for piecing. One other issue I noted when using poly both top and bottom for piecing is that I needed to be careful not to cut the threads too short. Poly thread stretches a little while sewing; cutting the threads as short as I do with cotton sometimes means I lose a couple of stitches at the very end (from the polyester thread springing back into the seam). The differences in thread combinations are subtle, but ones I appreciate, so using cotton thread both top and bottom for piecing makes sense for me with my current machine.
I recently took some classes with Jamie Wallen. He uses polyester thread exclusively for his machine quilting, in part because it stands up over time better than cotton thread does. The only time he uses cotton thread for his quilting is if the customer is a cotton purist and insists on cotton thread. Jamie said he has talked to many museum textile experts who have told him that they have many beautiful quilts in storage that cannot be brought out to show because the cotton quilting thread has dry rotted. This happens because most quilts end up being stored in less-than-ideal conditions (attics, basements) over time. The portion of the quilt most vulnerable to deterioration is the cotton quilting thread that holds the layers together. For hand quilting, I would never switch from cotton to polyester thread because it would be so much more difficult to work with. However, for machine quilting, it can make a lot of sense to switch from cotton thread to polyester thread.
There are so many options today, every quilter ends up making decisions about what they are most comfortable with. It used to be that the only "real" quilts were hand pieced and hand quilted with all-cotton components (mostly because those were the only options a quilter had!). Nowadays it's not so simple. There are many choices made at each step in construction, and each choice has pros and cons.