Sorry I didn't see this earlier.
Keeping in mind I have the 750 Sport, my 11S is an 01 the Duc an 01 and the two bikes are different niches.
The BMW is much more refined in fit, finish and ride (I have Olins on the front and back and the price points new were very different). The R1100S is a little more on the touring side but very capable in Sport mode. Something like 53/47 touring/sport in my estimation. I use mine mostly on the back roads in the PNW and "tour" farther out on the back roads to sport ride on new roads. Compared to the 12S the 11 is better for 2 up riding but I have never done two up myself. If I had the extra $4k when I got my 11S I would have done the 12S just because I know I would not do 2 up. The 11 is also much heavier that my Duc as can be expected 1100cc to 750cc. The power type is comparable with the Duc winning a bit on quickness, faster to rev up. In my opinion the 11S is prettier, much prettier. You can get quicker, faster and lighter in the same class as the 11S but they aren't an 11S IMO.
I love them both. The duc being relatively light but not as comfortable I use it for around town, commuting (when I can get it away form my son) and short 1/2 day rides. When I get a chance I will use the Duc for track days but that is mostly because of the $ invested in each.
I know I will keep the 11S but I hope to upgrade my Ducati ride to a Ducati with more HP.