Try filling the door seal channels with silicon paste/grease with a small paint brush. Ultimately what happens is the flocking wears off the seals and the glass rubs onto rubber, which causes binding and squeaking. It got so bad on my MK5, the one touch down/up didn't work. Cramming a f'ck ton of silicon paste into the seals fixed the problem immediately
Don't get silicon spray, get grease as it stays put longer. Sprays just wash away the first time it rains.
If you have a sunroof, use it on that as well to prolong the life of the runners.