Why would you want to upgrade the stock breaks? They brilliant.
granted the stock ones are going to be good, but they aren't the best
I agree. They don't have a particularly good "feel" at the pedal, and when the car is fully loaded, the standard anchors can feel everso slightly lacking, and in need of improvement.
uprated ones are going to have less fade and be able to stop quicker.
Agreed with less fade, but dont agree with stopping any quicker. You need to "think out of the box" to work out why. 
the only think i will say is if you do upgrade the fronts, do the rears too, otherwise you mess up the balance and your passengers will constantly eat dash
Actually, no. There is no need to do the rears. The ABS system has something called EBD, which means "Electronic Brakeforce Distribution". 
Oh, and to all the posters/lurkers reading this, Porsche have always had close working relationships with VAG. One of their notable projects was the original Audi RS2 Avant. Indeed, Porsche brakes is quite a popular upgrade.
...I agree with T_T:
Good, we are back to our harmonious state of mutual agreement!
The stock brakes can fade and pedal response is poor compared with something like AP's.
Whilst I havn't personally experienced any brake fade - yet, I do agree the pedal response is quite poor.
I'm told (by AP) that you don't really need bigger brakes on the rear because the GTI isn't that heavy for their front stoppers and most (about 85%?) of braking is done on the front.
All shortish cars, particularly hatchbacks are like that. Even on longer wheelbase saloons with big boots (trunks, for any yanks reading), normal braking efficiency is around the 30% rear to 70% front.
However, what is missing from those equations is the relatively new control and wildly varying distribution ratios caused by stability programmes. ESP does need to apply quite big forces to a single rear wheel brake, and it is not un-known for rears to fade!
Ray West's road 'n track 270bhp GTI has Porsche brake components on 19" alloys but he milled the bells himself. I've driven it and braking is awesome but still smooth. He's got an international racing licence and so needs that level of performance on the track.
Those rims are lush - who makes them?
