What years of both bikes?
There was a recent review of all the 04 big hitter bikes in a UK mag, and a couple 600 classers just to show how well they compared to some of the bigger bikes during the tests. It was a very exhaustive test with multiple riders, all the bikes at the same place/same time/same weather/etc... I really need to find the PDF of it, wish I would have saved it.
Anyway, if I recall in that review the 999 Duc and the 1000 Aprilla got lower scores due to just how well the Japanese bikes are performing nowadays, and honestly, I'd have to agree. Its becoming really hard to compete w/ the japanese in price/performance when it comes to sportbikes nowadays.
I believe the current RSV 1000 is completley redesigned, i'm sure its incredible to ride and I venture to say that it makes more torque...and makes it sooner...than the 04 R1 (or other 04 japanese liter class for that matter). Of course, once in the gravy zone....the modern I4's will likley out run it.
"Jesus has my heart, but Whiskey has my liver" --Jason Boland