In anything with curves, the R1 or any of the recent liter bikes will pull away from a Busa. Better cornering, better lean angles, faster transitions, much better brakes -- in short greater agility. Any of them will be far better/faster than the Busa on a track or twisty road.
At the 1/4 mile, the Busa will still have an advantage. Its longer length and weight help keep the front wheel down so that more energy can be spent on accleration. Plus there is a sizable torque difference between the liter bikes and the Busa, especially at lower RPMs.
Top speed will probably still remain the Busa's playground. The aerodynamic differences really come into play at speeds over 150 MPH. Even with the peak horsepower numbers (at the rear wheel) on the new liter bikes being about the same as the Busa, wind resistance and drag issues will hold them back. Of course the top speed issue is moot, since all the bikes are limited to 186 MPH (or 300 KPH if you prefer.)
All of this assumes stock bikes with equally skilled riders. Starting making mods or improvements and things could change a bit. And a good rider will generally smoke a less skilled rider. A good rider with a seriously extended swingarm on a R1, might well smoke a stock Busa in the 1/4 mile.
hmmmm.... well i got my r1 extended 3 weeks ago and i kill my friend who has a busa but only to like 145 then he catches up and flys by.. i was thinkin replace my clutch since its slippin and put NOS 50 shot ... what then will i take him??