I traded a 98 ZX-9R for an 01 R1 just this spring. I've had 3 years on my 9R, and about 5 weeks of riding on the R1. From a handling standpoint the R1 is definitely a big step up. Noticably lighter, much quicker turn-in, still working on dialing the suspension in. Had the stock suspension on the 9R dialed in pretty good, it was very predictable. Even with unoptimized suspension the R1 still handles better at this point.
With regards to power though, calling the 9R a dog is simply asinine. I haven't lined both bikes up for a shootout, but the differences are no where near expansive enough to even think of calling the 9R a dog. I really don't want to insult anyone here, but that's just... ah screw it.