I owned a 5 speed 2000 Jetta for about 7 years, bought it used with 4,000 miles on it. Overall I was really satisfied; never had any major malfunction and never got a Check Engine light on. Drove it for about 50,000 miles. I actually bought another one but automatic when I passed this on to my wife. Same good experience overall. However, did experience the issues with the locks and windows. Very hard to diagnose and repair. Fortunately got guidance on how to repair them by myself in a VW forum and fixed them all, but was hard nonetheless. It appears to be that after reaching the 8 yrs threshold, soldering joints in the electronics start to fail.
Overall reliability was very good, never had issues neither with the engine nor with the tranny on both cars. Good performance. I drove both cars in Mexico City in heavy traffic, never an issue. Most serious problems reported might be due to severe weather variations affecting the electronics.
Interior quality in some dash and door trims components could be improved. Power windows mechanism is indeed deficient, regulators should be stronger. Unnecessarily complex locking mechanisms prone to failure.