In the long run, cotton & poly break down at different rates and fade at different rates. If you are asking about 20+ years into the future, I am a fiber purist and believe in using all the same fiber for fabric, thread & batting. That said, cotton will start to break down around the 20 year mark & you will likely need to do restoration regardless of whether you mix & match fibers.
I did mix & match on my very first quilted projects & it held up fine for the first 15+ years even with improper washing (washing in warm, drying partway on medium heat). Yes, threads have improved during that time, but at the end of the day, polyester is a long-chain polymer and cotton is a natural fiber. Advances in the science of creating synthetic fibers has made poly threads that feel softer, that have smoother edges so as not to "cut" into natural fibers as much & that better mimic natural fibers straight off the assembly line, but as far as how it retains color & breaks down, it will always behave like a synthetic fiber. If you pick a red poly for one thread & a red cotton for the second, over the decades the red cotton will fade to a dull red & start to fray while the red poly is still nearly as bright as day 1 & almost as strong.