I came to the Jetta Wagon from a Civic and it is I came to the Jetta Wagon from a Civic and I have to say that it is a much better car. The cargo capacity is incredible, especially considering its compact size. However, like many European cars, it suffers from electronic gremlins (most of the issues, solved under warranty). More worrying was extensive cylinder work at around 50k miles and a rebuilt transmission at 70k, the latter, according to internet forums being a common issue. Despite its practicality, its comfort and attractive design, I would not recommend that you buy a second-hand one. I am trying to get a couple of years more of mine and will move on to a different brand.
If it makes you feel better I have a wagon. This car would be a great car if all the parts could be shipped next day from Germany. Good luck with your transmission. You can start thinking about replacing it at 60,000 miles. The tiptronic switch is easy to replace if you're a mechanical geek but if not it will cost you around $500.00 to fix. This is not the kind car you buy parts from your local part store. Be ready to get dirty and learn how your car works or pay a hefty price at the shop and I'm just talking about your regular maintenance. If you can afford the upkeep of an Audi then go for it because that's what you're buying anyway.
I really anticipated this being a car I could drive forever (at least to 150,000). Volkswagen has lost a customer. This car was a lemon. A nightmare. Last year I spent 3500 just keeping it running. All the problems everyone else reports are true! Small random pieces falling off everywhere. Cheap interior fabric ripping on, replace ac at only 75,00, break problems, tire wear issues, Burns oil like crazy, failure to shift properly, transmission issues, lots of noises. At 95,000 miles it started blacking out while I was driving, a terrifying experience. Had to cut my losses and let it go. All the while having these problems, the mechanic laughs and acts like I am crazy. Do not buy a VW!
I have a 2002 Jetta 1.8T Wagon with the 5-spd manual. Great car - it's fast, quiet, comfortable, has an interior that looks and feels expensive, and handles well. PLUS it has the utility of a small SUV! What more could I want? I'm the sort of person whose lifestyle would be well served by an SUV, but I wanted a real car with real performance and handling - this car fits the bill to a T.