I wouldn't rule out the MAF sensor too.
Should take complete logs; channels 001, 003, 004, 008, 011 to determine where the problem might be coming from.
Yesterday a customer with a 2006 TDI and low km (20k) had timing issues after getting chipped. It was a little jumpy. The power felt good & smooth but VAG-COM logs didn't look perfectly normal to me. We went ahead and swapped in a fresh fuel filter. Problem solved.. if the fuel filter was neglected and had continued to clog further, the power will gradually drop over time.
evangelos: Do you have VAG-COM? If not, find someone who has it. An aftermarket VAG-COM cable can be obtained for $20-25 USD approx. if you already have a laptop. Let me know if you want your own cable.
Open VAG-COM software, log in Engine-01, click Measuring Blocks.
Select one of the aforementioned channels ONE at a time. Begin logging at 1,500 RPM in 3rd gear and then floor it until 4,500 RPM. Stop logging at 4,500 RPM. Do the next channel until you're done.
Go to C:\Program Files\VAG-COM\Logs\ (or wherever your VAG-COM folder is). Save the log files and post them here or e-mail them to us.