I have a 2001 Polo 1,4 which is a very good runner. I am told that the breather pipe from the engine to the air filter can get blocked with gunge, which could result in the symptoms you describe. Worth a try - and quite a simple task. Also have you changed the plugs ? They go for 40,000 miles without attention so they could be due for renewal. Not cheap at �35 a set but e-bay worth a try.
But it sounds like the car needs a good service with the engine electronically analysed. Keep well away from VW main dealers, they're expensively useless. I'm lucky to have a VW specialist nearby and he's honest, reasonable and a VW whizz kid. Good Luck,