I have had very few serious issues with my 03 Jetta, but it is a TDI. I can't speak to the gas engines
I had to replace the manual trans at 310,000 miles due to the differential bearings going out. had to put a clutch in at 105,000. obviously due to the woman that owned it before me, as I have about 210,000 on the one I put in. I have done plenty of normal maint items brakes, wheel bearings, shocks and such. but the car has been fantastic for me!