I have a 2017 R1M (new April 2017) and a 2016 S1000RR (new March 2017). The brakes on the R1M are weak. Just riding it from the dealer they were obviously not on par with the RR. I also hate that you can't downshift without the clutch. Straight valve stems? Say it ain't so.
R1M feels better in high speed turns, but isn't as nimble in low speed turns. Power down low (and everywhere) goes to the RR. R1M gearbox feels better. R1M seat feels like a plank of wood. Seriously.
If I had to pick one, and price was even part of the equation, I'd pick the RR. Honestly, with price out of the equation I'd pick the RR. I'll be playing with the brakes some, but I've just about decided I'll trade the R1M in on the new Aprilia/Honda and probably get the new RR as well.
Hopefully my V4S will be broken in soon.
San