I think the '99 2.0 is the most reliable of any of the New Beetles. No turbo, which adds a lot of complication. No immobilizer, so a lot less key/no-start issues. No '98 quirks, since '98 was right in the transition from Mk3 to Mk4 on the chassis platform. Still has the throttle cable, so no drive-by-wire.
The timing belt, water pump and thermostat are most definitely overdue if they haven't been replaced. You don't want to drive very far before those are done. Timing belt failure can destroy the engine on the New Beetles.
Also, check over everything electrical on the car: power windows, door locks, operation of the door latch (
http://newbeetle.org/forums/questio...ms-new-beetle/59654-door-latch-resources.html), exterior lights, dash lights. These can all point to more serious issues. Switches with notable reliability problems are: ignition, headlight, turn signal (check while using cruise control), HVAC fan speed and
every one on either door panel.
Scan the engine for codes (preferably with a VW-specific scanner to get the manufacturer codes, not just the generic).