Personally Id take the S3 just for the sake of a but of a change as MK6 is very similar.
Best advice I can give is to take both of them for a test drive. Some people have commented that the S3 can be a bit "boring" to drive compared to the GTI. How they came to this conclusion I dont know as I'm yet to have the pleasure of driving a newer shape S3. I think they are lovely cars and would love one after the GTI (need to wait for them to come down in price).
I wouldn't take power into account as for ROUGHLY 1ks worth of mods a GTI will keep up with an S3 (but then the S3 has "4WD").
lmao @ ub7rm, you got issues mate