When I bought it, the gear stick was loose and you had to put it in first or third gear before you could shift it to first gear. The previous owner (who also bought in used in 2000) thought that it was normal and found it amusing that it shifted like an old VW bug. I took it to the only authorized VW service center in Metro Manila and there was no parts. (some kind of bushing) As of this writing, The gear stick still sucks and there doesn't seem to be a way to fix it without that simple bushing thing...
I found the clucth also too low (when shifting) and too high (when releasing). It took a lot of getting used to. I took it to the service center to have it adjusted, but they claimed whether the clutch was new or old it cannot be adjusted and they gave me a quote of about US$500 for the entire clutch assembly (plus installation). I thought it was pretty ridiculous so I went to an independent VW specialist and now it is running splendidly.
The left rear power window doesn't work. Again, the VW shop said the mechanism isn't available per piece and you had to buy all four power window mechanism sets for about US$400! I guess since they are the only authorized VW shop who has a large inventory and German trained specialists, they take advantage to a diabolical level.
The two rear speakers are grounded and barely squeeks out the tunes. I was told only the blaupaunkt place can fix it (every one else is afraid to touch it).
The polo also has a lot of blind spots and it takes a lot of getting used to specially in the wild and crazy traffic of manila.