I'd still bet on it being the MAF even if it gets worse by unplugging and even if it doesn't show up on VAG COM.
My TDi Bora had exactly the same symptoms, engine felt strangled above 2500-3k rpm. There were no VAG COM errors and it was worse when I unplugged the MMAF, yet it was at fault, I only found out when it eventually went completely and ran like a complete dog.
The really annoying thing with this particular failure was a few months earlier I swapped the MAFs over with my missus's TDi Leon and it didnt improve, so I assumed it couldnt be the MAF. It wasnt until the Bora MAF died completely and I got a new one that I found out that the one in the Leon was also faulty!