I have owned both an '09 1125CR and an '09 R1. The R1 obviously has a lot more straight line speed and is fantastic overall, but the 1125CR was a much better handling bike, no question. Much easier to ride, quicker steering, excellent brakes (although my R1 brakes are much better than OEM with the simple addition of Ferodo pads), very user friendly. I've got Q2s on my R1 and a 3mm shock shim to speed up the handling, but it will just never be as easy to ride as an 1125 down a twisty back road. If you think I am crazy, look back at the 2009 AMA Daytona Sportbike races where Eslick on his 1125 routinely competed against and beat R6s, GSXR600s, ZX6Rs and it was NOT because he had more top end hp. The 1125 can corner with the best of them.
In my mind, the Buell and the Yamaha are two different flavors of the same sportbike ice cream. Both great fun in their own ways.