Oooh, tough one. I would have looked more seriously at an R6 if it wasn't for the Suzuki insurance deal. I think the R6 looks way more aggressive, the only thing I have a problem with is the standard can (the one on the gixer looks better as standard to me).
IIRC they both rev to the same amount (R6 was supposed to be 18k but then Yamaha admitted to a reading error with their counters, no? So it was actually 16k) so no difference there.
A mate of mine sat on an R6 though, and the tank stuck out too far and obstructed his arms, compared to a GSX-R600.
Are you actually going to buy one or are you just asking questions?