I'll be the first to admit that the 77x53.6mm 5-valve motor in my R1 does not have the same area under the torque curve as compared to the 73.4x59mm 4-valve motor of the '05-'06 Gixxer 1000. That said, I've ridden WITH those bikes.
My Hayabusa vs. '05 Gixxer 1000 experiences include race track AND drag strip comparisons, including a VERY telling experience at the drag strip against a very well prepared Supersport race-prepped '05 with a top local (as in AMA pro racing capable) rider, alongside my Hayabusa (valve cover never been off), and I dumped him like a dirty shirt. At the drag strip, the additional 2.6" of wheelbase allowed me to get the jump on him, and at the race track, the aerodynamics of the Hayabusa causes them to fall out of my draft above 150 mph.
My R1 vs. '05 Gixxer 1000 experiences include race track AND drag strip comparisons as well. In the interest of fairness, I should note that my R1 is equipped with a full aftermarket racing exhaust that eliminates the "EXUP" exhaust flapper valve- with a decent map in the Power Commander, it fills in the "hole" centered at about 7,500 rpm, to the tune of about 20-25 horsepower (no kidding!), although the bike only gained about 6 horsepower up top. The '05 Gixxer 1000s are CLEARLY faster than the pre-'05 models. At the top of the powerband, they are comparable enough with my R1 that it obviously comes down to differences in skill between riders (as it often does in these types of situations). On the drag strip, I've done surprisingly well against them. On the road racing course, I've had them get away from me, and I've had them not able to keep up- either way, the bikes themselves seem pretty close.
To the average street rider, I'm sure that the light weight and low-rpm power of the Gixxer makes it feel really powerful, making them a lot easier to live with (especially if you gear them down a little), and the short wheelbase isn't as much of a problem, because you're not doing 8000 rpm race launches.
Due to it's shorter wheelbase, the '05 Gixxer 1000 is never going to perform like the 3.2" longer Hayabusa through first gear.
And due to the Hayabusa's better aerodynamics, the '05 Gixxer 1000 is never going to perform like a Hayabusa above about 150 mph.
The narrower engine and lighter weight of ANY 1000 makes it a better choice for EXPERT level ROAD RACING.