I have both an 1199R and an S1000RR. I'll give you my thoughts, though to be fair, it's not a fully apples/apples comparison as my S1000RR is all set up for the track while my 1199R is all stock with exception of the Termis (ok, those are stock on the R), fueling, and stiffer front fork springs.
I rode both at Portland International Raceway, my home track. I also rode the 1199R at the Ridge raceway in WA.
What I found on the 1199R - it looks and sounds great, very good brakes, agile handling. Very good transmission and shifting. The main problem that I had with the 1199R was on the brakes. Even with the stiffer springs I was bottoming out going into T1 at PIR (almost mile long front straight) to the point the tire was rubbing on the plastic piece between the radiator and oil cooler. If I turned up the compression it would start to get a nasty mid-corner chatter as you approached a 9/10's pace and didn't give me much confidence. To go faster it would take some suspension work. The agile handling also turned into a bit of nervousness and amplified mistakes, especially towards the end of a session when you get tired. The motor was fast, I could keep up with stock S1000RR's on the straights. Engine braking was surprisingly strong, I'd recommend using setting 2 or 3 for the track. Traction control was at 1, but still a bit too intrusive. Fastest time at PIR was a 1:10 with Dunlop slicks.
As far as my S1000RR - it's all set up for track duty with good suspension, bodywork, exhaust, etc. It is very comfortable to go fast on, stable but also turns in well. Very good brakes like the 1199R, but faster down the straights. The one big handling issue I have is coming off the corners I sometimes get pumping from the rear shock. It's really bad on PIR's bumpy "back straight" T6 with the traction control light constantly flashing while you're going 150 mph! The TC is a bit better than the Ducati, but I have the kit ECU that comes with the German IDM Superbike series settings. The shifting is not as good as the 1199R and prone to false neutrals if you're not deliberate with the downshifts. My best lap time was a 1:06 on Pirelli slicks. For reference the current lap record at PIR is a 1:05.
For me I would take the S1000RR to race because it's easier to go fast on. I'm sure the 1199R can be made to go very quick, but I think it would be a lot pickier on set up. I will still ride the Duc at the track and have a lot of fun with it, but for racing I would choose the BMW.