I've been pretty happy with my '06 Jetta deisel. I did have a problem with a faulty clutch cylindar which the dealer replaced under warranty. Also, the radio is crap: it routinely loses the XM presets, defaulting to the preview channel. Sometimes all the buttons on the face freeze and I can't change any station. I've told the dealer about it a dozen times and they keep telling me that unless VW issues a recall for the units, it's my problem.
I also don't like having an engine cover on top of the engine. Sure, it looks great. But when I wash the car and wipe off the cover of the engine, I know I'm not keeping the engine clean at all, since it's under that dang cover.
Other than that, I'm very happy with my car. When I drove the E-320, I got about 250 miles on a 16.5 gallon of high test fuel. Now I can drive 470 miles around town on a 13.5 gallon tank of diesel. What I'm saving of fuel costs alone more than makes up for any misgivings. The car looks great, has a nice interior, and is a blast to drive!