I replaced the starter twice since I bought it in 1999.
I replaced the ignition switch in 2004 because the headlights and windshield wipers occasionally stopped working.
Inside door locking/unlocking switch hasn't worked well since I bought the car.
Fog lights are no longer functioning.
I replaced the cruise control.
I had to fix the locks, which stopped working properly and led to difficulties starting the car.
If I open the trunk and the doors are locked, the alarm goes off.
Cosmetically, the door molding started to come off on both sides, so I glued them back on.
I've had major paint problems. My car's red paint started to oxidize. I waxed it, and it looked fine, but then the oxidation reappeared about two weeks later. The dealer said it was probably repainted in the factory. It was past the warranty, and VW wouldn't cover a new paint job. (I didn't by the car from a dealer.) I've noticed other similar paint problems on other red Jettas.
This is my second VW. Performance-wise, I love it. I changed the suspension and bought a new exhaust, and my 4-cylinder Jetta drives really well with these modifications.
Electronically, the vehicle is a mess. I've been really frustrated with the locking problems, and VW refuses to disarm the alarm, which I think may be part of the problem.
You should check the wires in the door jam, they may be broken and causing your alarm to be a bother.