Because the 2.0L is a low power economical base engine and does not have much in the way of cost effective vs a substantial power upgrades benefit (e.g. cams, neuspeed super charger and much more expensive turbo upgrades etc), I would just keep things stock. The stock airbox is said to not be very restrictive, brings in cold air and doesn't have issues with water ingress and engine hydrolocking.
If you wanted a improvement in breathing with the stock airbox; a k&n drop in filter, does add a better throttle response/acceleration, for about $50. I have had this type filter on my1.8T, for many years and I think it is a good compromise; in keeping the stock airbox intact but improving the breathing/throttle response of the engine.
Long term, if you want a higher performing new beetle and a good foundation for performance upgrades; i would sell the 2.0L model and upgrade to a Turbo S model with the 180 HP 1.8T AWP engine and rhe six speed 02M transmission.
