It may be a personal thing but I like the idea of owning the best of the breed, and it will be worth more in the long run than the S. Maybe not much given they are the 999 shape but you know what I mean.
Plus you get all the goodie's with them, carbon this that and everything else, a few extra ponies. Just beware the service intervals, I may be wrong, but I believe they're shorter.
I would personally take that cash and get a 998R or a 996R and use the money you save on presents for it.