Faults:

Power window switch broke.

Side view mirrors' heaters are not working.

Driver's seat heater is not working (to fix it would need new heating elements inside the seat).

The engine bay is cluttered, not much room to do maintenance. Requires patience. Permanently removing the plastic engine and battery covers makes 'em easier. And once you get hang of it, you'll know exactly where to put your hands.

The tires/rims are quite big -> getting decent quality tires will cost quite a lot. Especially northern Europe's winter/studded tires.

The trunk itself is awfully small, barely fitting your shopping bags. But if you don't have passengers on the back seat, you can flip the seat down and get wide space for even small furniture.

The car is heavy, so the stock rear disc brakes are little bit too small and heat up very easily in harder driving. It needs bigger, vented discs in my opinion.

Fuel efficiency is bad in these times of high gasoline costs.

General Comments:

The car is mechanically similar to the same year's Golf IV models, which are very popular, so the parts are easily available everywhere and are relatively cheap. But the New Beetle specific parts, like interior or body, they can cost a lot.

The seats are very comfortable, you have huge amount of head space -> fits perfectly for taller people. Also, very short people can also find surprisingly good seating positions, thanks to the wide adjustment possibilities.

The handling and performance is brilliant and sporty. If the car is in good condition, you feel like you're driving a bigger and more luxurious car than it really is.

Small but important thing: The windshield washer system is excellent - wide blades and high water pressure!