I used to be a member of a sportbike club so I've had the opportunity to ride a bunch.... but of course, my opinion is just that - opinion. Every rider wants a different set of attributes.
Having said that, I personally chose a Yamaha R6. I preferred the riding style, and it has one of the more comfy saddles for longer rides. The electronics are bulletproof, the engine is an engineering masterpiece, and the handling is razor sharp. I found myself a little faster on a GSXR 600, but it wasn't as comfortable or forgiving as my R6 in my opinion. Its just not quite as refined as the R in many of categories.
I also chose against the bigger engines. I'm 250 lbs, but the 600 was still way overkill. Even if I'd lay my weight over the tank as far as I could, the front still came off the ground in first. The larger displacements counteract their power with pretty insanely high gearing and sprockets. I got so frustrated on an R1 and a 'Busa trying to get started from a light. High-revving, low torque engine coupled with high gearing = frustrating on the street. Its just like a Corvette. You can get them with 600 hp, but they have a 2.73 rear gear so that people don't kill themselves. I'd rather have enough power and the streetability to go with it. R6 for me. More than enough power, great street manners, killer ride.
Get an 04 or later bike; the earlier ones had gearbox troubles. In first and second they would skip a tooth every once in a while. Not good exiting a turn when the rear end kicks out on you