I own a 2009 2.5 (auto) Sportwagen, and so far it's been great. No issues or problems. I mean, when it's cold outside (-15) you'll hear some squeeks from the dash, but really, what care doesn't experience that from time to time? Brakes are still holding on, and the transmission is as smooth as can be. We use it for city and long distance driving, and it beats out any SUV for space functionality. Service at the dealership has been great, and with an extended warranty, I'm feeling alright about the next few years.
No car's perfect, and the previous generation had more than its share of problems (I had a 99.5 Jetta GL, so believe me, I've been there). But Consumer Reports has had a lot of positive things to say about the Sportwagen, especially the 2.5, giving it "Above Average" reliability. Hope it keeps at that level, but my experience over the past two years has been great.