You're pretty lucky as the mid box and back box are the only parts of the exhaust that VAG still have in stock, and according to my local dealer, there aren't many of those left.
Standard all the way for me, but it really depends whether you want a roar or a purr. The VAG system is supposedly pretty durable too. Don't forget that a stainless system will add extra weight to the car too, for relatively little performance gain.