At my first oil change I complained that the shift lever was violently shaking in 4th gear, so VW replaced the shift assembly. Things went well for a few months and then the shaking came back. I brought it back to the dealer for the 10k checkup and told them the shaking was back. To my amazement they told me they had to rebuild my transmission!! This should never happen with a manual gear box, especially one with 9500 miles on it. But it doesn't stop there. Today the automatic up/down feature for the windows stopped working. I've owned the car for a year and put 9500 miles on it and it has been in the shop for over 4 weeks in one year...not a good ratio if you asked me.
Fit and finish. The car really is amazing inside and out...you feel like you are in an Audi, not a car costing $16k. There are also a bunch of niceties that you don't notice until they kick in (e.g. the rear wiper turns on automatically when your wipers are on and you go into reverse).
I only have two complaints, MPG and build quality. Having only one engine option is crazy, especially when it's a 2.5L. There's like 10 engine options for the Golf in Europe. I think with today's technology one should be able to buy a car and have it be free from any MAJOR problems e.g. bad tranny