Ah, comparing the FJR to the Busa. One of my favorite topics!
When it comes to comparisons; I think bikes are very much like cages. There's mini-vans for families; Mustang's, Vet's and Viper's for people with a need-for-speed, and a whole slew of other various boxy sedans and SUV's ranging from mild to wild, for everyone in between. Selections for comparisons need to happen carefully.
I'm very lucky, blessed, or probably both. I own both a Busa and FJR; both 2005's, and feel I have the best of both worlds. My goal was to own a comfortable, yet fast & fun, good handling touring machine that I could take on extended trips, and at the same time maintain a nice level of "sporty'ness". I also had an urge to own the fastest production motorcycle on the planet. Certainly one motorcycle wasn't going to fill both of my goals. Here's my take on the FJR and the Hayabusa.
First I'll answer the thread question; "How much faster is a Busa then the Jeefer?" The FJR has excellent acceleration, but the Busa will dust it easily. The FJR will be in the Busa's rear view mirrors nearly instantly, and remain there until the FJR is out of site. Just twisting the throttles of both these machines, while sitting in neutral, will let you know the FJR doesn't stand a chance against the Busa. The R's seem to rev so much faster on the Busa. The Busa's engine feels like its begging to be run (and run hard). In comparison, the FJR's engine provides nice "pleasant" sounding rev's, but doesn't rev up nearly as quickly. An interesting thing about the Busa engine is, once you're rolling and pore on the throttle, it NEVER seems to give up. It just keeps pulling harder and harder. Clear your path, twist the throttle, tuck, and hold the frinkin' hell on!
But getting back to the comparison, these two bikes are not designed to do the same thing. Comparing the FJR to the Hayabusa is like comparing a Lexus LS400 to the C6 Corvette. Both quick cars, but you'd never see a magazine do a comparison of them.. There's just no logic to the comparison at all. The FJR and Busa each has their pros and cons, reinforcing the basic fact that, "there's no one perfect motorcycle (or car) that can do everything perfectly." Engineering design trade-offs, are key here.
Saying all of that though, of every bike studied the specs on, and/or driven, I'd have the say the FJR comes closest to being the most perfect "comprimize" motorcycle there is (IMO).
I love both bikes for what they do. As far as I'm concerned the FJR has really nice advantages over any other sport/touring machine; nice adjustable wind protection, decent level of comfort, excellent acceleration (plenty enough to keep things fun), good solid handling, and with the top box and hard bags installed - plenty of storage. I'd select the FJR over the Busa if I was taking a longer trip, (in a NY second!). The Busa is not a super-comfortable machine. It's been my experience that the Busa is a bike that I had to "learn to adjust to", (but it's well worth it!).
If you throw all logic out the window (comfort, storage, wind protection, and other practicalities), and speak purely "fun factor". On a scale from 1 to 10, I'd rate the FJR at most an 8. The Hayabusa, although not nearly as comfortable as my FJR, definitely rates a 10 in my book. R1's and other 1 liter lighter sport bikes probably rate right up there too, but don't they have the rock solid stability that the Busa has, especially at its higher speeds. Then again, 1 liter sport-bikes have a high flickability factor, which some find a priority. It's all about design trade-off's.
I find the hardest thing about piloting the Busa is properly managing the right grip. It'll definitely bite the s### out of ya (as in: quickly hurt or kill) if you're not careful to maintain a healthy respect for its power. (There's not that concern when I ride my FJR.) But as your experience and confidence grows it's impossible to explain how exciting this bike is to pilot! It's my guess that most people's courage runs out waaaay before its acceleration does. Twist the throttle hard on the Busa and the acceleration will impress (and scare) just about anyone.
After a ride on the FJR I feel really good; park it, maybe give a once-over-cleaning, then go about my business. After a ride on the Busa I find myself smiling for a couple of hours afterwards. I clean it to where there's not even a sign of dust on it, preparing it for its next flight. (Then sneak into the garage now and then to take another glance at it.)