Okay, so I own a 2015 R and in no way apologise for my bias as I adore it.
Sadly I've never had the priviledge of riding the Desmo, but I've seen and heard one myself, although side lined as it was too loud for track!, and I have to agree with what's been said here already, it truly is something else, it really is a little bit special, no denying it, hands down beats the R. I have to say this because the Panigale has the charisma of an iPhone, but that is down to Mr Ducati's marketing. 1199, 1199s, 1199r then 1299, 1299s, blah, blah, blah iPhone 5, 6, 6s, 6Plus.......... you see what I'm getting at. The Superleggera was special, but never as unique as the Desmo.
However, I as for the machines themselves, again the Desmo has some incredible engineering under it, but so does the R. A V-twin revving to 12,500 is just magic, it's intoxicating, you have a fistful roaring up to 10,000 rpm and the speed it revs up, thinking this is great as it boots you up the backside and gives you more, incredible!!! The R is much prettier in my eyes too, I sometimes find myself just looking at it for quite a while. I've always loved the Panigale in this respect, the lines, single sided swing arm, low slung exhaust etc. just the noise too. But it did take two previous incarnations of Panigale ('12 1199s and '14 1199r) to get me to this particular model that I'm finally happy with.......
Well, if I'm truly honest, I have the set up with mechanical suspension etc. but the engine is too much for me. But, you don't have to floor this bike everywhere to enjoy it, just how it behaves and the noise is just sublime. Small commuting miles are no biggie either if that's what you plan, gearing for high end power actually makes this a kitten and very managable round town in low rpm with no issue.
So for me, the R, all day every day to ride, to use, to enjoy. The Desmo would be a nice to have, a second bike, a wall piece, a f*cking big WOW in your garage.
It's nice to have choices....... *cough* Superleggera, did I say that?