well, in like 3 of 4 mags, the 6 came out on top. no reason for that to change this year since everyone brought the same toys out to play this year.
nonetheless, it comes down to how comfortable you are on the bike and if you like how it looks (and probably at some level, insurance, since the R6 was the most stolen bike last year - I believe anyways) etc, etc. Both the 600rr and the R6 are great bikes with a ton of aftermarket support for them. Obviously I'm a bit partial but I sat on both and was really uncomfortable on the 600rr. To me, thats just one more distraction I don't need when I'm on the road. I got enough to do with checkin out the cars and trying to figure out what they are gonna do so I can avoid them (cuz they are all idiots out there) instead of sitting there thinking about how hard the seat is or how aggressive the seating stance is. The R6 handles like a dream and has great power delivery (I can only speak to the 03+ bikes) along with great brakes. Hell, it damn near ran the sames lap times as a Suckzuki 1000!
So, personally, I'd say get the 6. But the choice is ultimately yours cuz you gotta be happy with what you spend your money on.