I'd take the R!
Oh, I did
The R has newer electrical architecture. The S3 is stuck with the old RNS-E as a result. The red dash lighting on the S3 doesn't look high quality like the Golf R's white and blue, plus the overall styling on the S3 is based back to 2005. Newer S3's do look much better than the older style ones, but still don't look as sporty as the GolfR. I've driven both and the R feels better, I know there shouldn't be much difference, but there is.
The main factor is a Golf R is cool, the S3 isn't bad, but not really a cool car with the Audi stigma attached to it