I owned a '15 R1 and a '15 S1000RR at the same time. I was a victim of R1's do not ride transmission recall. That year was also the year BMW had a problem with forged rims on the Premium edition and put cast on many of them. The BMW has always been perfectly reliable for me.
Riding position style the two are very different. The R1 you're on "top" of it, and the S1000RR you're "in" it. The tank shape is primarily what causes this feeling. Personally I'm faster and more comfortable on the S1000RR (12,15). The previous gen R1s were all "in" it style bikes and I loved those (01,02, 04, 09).
Someone complained about torque on the R1 and no idea why...I had full system, FTECU flashed with autoblipper and the bike was a monster out of corners. That said, its throttle was a light switch, whereas the BMW I felt as though it was connected to my brain directly and super smooth. These are style preferences, some prefer that light switch type.
Cruise control is that awesome, same with heated grips.
The R1 is without a doubt lighter and turned in a bit easier, but the S1000RR is not a hog and carves corners smoothly just a bit more input needed.
R1 gets the nod in exhaust sound if that is worth anything to you.
Hopefully this is of some help and feel free to ask me anything. Ultimately there isn't a wrong choice between the two, hence my garage for a few years with both