Considering they are both incredible performers, I looked at some other areas.(1) Fit& Finish: The R6 Clearly has a better quality of fit and finish.(2) Feel: Both the 2001 600 and 750 GSXRs that I rode felt heavier with less feed back than my 2001 R6, even though they're all around the same weight.
They are both pretty much the same in terms in comfort and performance, to the casual person anyway. But if you're leaning more toward performance, go with the Gixxer. If you're leaning more toward comfort, go with the R6.
But it all comes down to personal preferrences. Sit on both of them.
The R6 and the GSX-R are about as different as bikes can be. The R6 turns in ultra-fast and offers tons of feedback, and really requires a high level of skill to operate. The GSX-R, on the other hand, is not a quick-turning bike, mainly due to its more conservative steering geometry and steering damper. The trade-off gives the Gixxer tons of stability--it never gets out of line. The R6, then, is the opposite. A steering damper is a very good idea for that bike, since it has such radical geometry and so much power in the upper part of its powerband.
my pick: the gixxer. It's not as sharp and agile as the R6, but it's got a howling motor, is awesome on the track, and not everyone has one. You see a blue R6 every time you go riding, those things are everywhere.
Either way, you can't lose with either one. It's nice to have such awesome choices!