Your comments sound contradictory. You poke fun at the gold forks of the "S" (the forks are different between the standard and the "S" as you know and not just color), yet you put BST wheels on your bike and a Termi exhaust on your bike and imply you don't take your bike to the track. So why make those changes? Because it looks good and makes you happy?
You've got more into your "S" than the cost of an "R"…
I'm not bagging on you or your bike. Its yours do what you want and do whatever makes you happy! Its just your comments don't take into account for the person like the one person above who would buy the "R" just because its totally what appeals to them.
Hell one day, I'm going to own a Desmosedici, and it may never turn a wheel on the track… I just want one!
I'm constantly amused by the reactions on this forums to something people don't feel is "the right answer", then it all goes downhill into very entertaining threads.
If you really want to know, and if it helps the original poster (even though I've made it clear which bike he should buy for what reasons):
Termi pipes don't add any significant hp - they just look and sound better. This will make any owner happy. And I only bought them after a year of 1200S ownership because I got a good discount on them (Don't buy them at original retail price)
Carbon wheels don't add any significant hp - they look subjectively better and help the bike spin up or brake faster, and make turning very light because they reduce the weight of the wheels by half (yes, even compared to the R forged aluminium ((not magnesium for the price)) wheels). This is useful for both commuting and track.
The Termis and BSTs are both available as upgrades for the R, S or base model, and they do not offer the specific track performance upgrades of the R engine or chassis or seat height. But they make your ride much more fun.
And no, I don't bring my bike to the track because it's my daily commuter and I would get a cheaper track-focused bike like a used Daytona if I really wanted to. And no, I don't think it's necessary to make the Monster into a track champion - there are other non-naked models that do that much better. Any bike can go on the track but Ducati is trying too hard to compete where it needn't.
And finally, if you're going to drop that much money on a bike, it'll be nice to have gold forks instead of boring black forks.
I was happy with my 1200S as stock, and I'm happy with its upgrades. If you have the budget and like to go to the track, go for the R. Otherwise, go for the S. If budget is a concern, go for the base model.
I hope this long-winded answer is satisfactory.