Well, I've yet to hear a stock head unit on the gti, but from what ive heard it has some type of protection built in to cut the volume when too much bass is being played..
This is not the case with the navi head unit, I think it sounds pretty nice. Although I have a couple regrets by choosing the factory navi.. (Don't get me wrong, I really like the navigation - being a nice clean integration as opposed to an aftermarket unit - directions showing up on the readout between gagues and such) but when choosing the navi you loose mp3 playback capabilities) Also, I dont know how much youre into audio systems, but I miss my alpine deck, & nice speaker setup I had in my last car..I think by choosing navigation you're really choosing to have that unit for the life of the car.
Being so expensive, I dont think Im ever going to replace it with an aftermarket. My poor alpine is just sitting in my closet... ..just looking at me every morning ...all sad ...its soo sad