The Big Bore Bike Vs. Litre Bike controversy. I'm only comparing litre bikes against 99-07 Hayabusas and 06-08 ZX14s.
Here is my take from many years of experience. Early years I do not mention R1s or CBR1K as they really didn't show enough promise till 05 and up. Also assuming rider weights are the same or within 10lbs. Stock to stock. Modified on any bike can change the outcome by a little.
01-02 GSXR1K Vs. Hayabusa >>> Hayabusa wins from Dig, Roll-on, etc.
03-04 GSXR1K Vs. Hayabusa >>> Hayabusa wins " " " " " "
05-06 GSXR1K, ZX10, R1, CBR1K Vs. Hayabusa >>> Hayabusa wins from Dig, Most litre bikes win on roll-ons
07-08 GSXR1K, ZX10, R1, CBR1K Vs. Hayabusa >>> Hayabusa wins half the time from a Dig, ZX14s win from the dig, litre bikes win on roll-ons(the GSXR1Ks are quite a bit heavier than the 05-06 and probably run like the 03-04s)
Most big bore motorcycles have big riders. Ranging from 200lbs to 350lbs. A lot of the litre bike fiders are 100lb to 200lbs. Yes rider skill can play a part in outcomes but sorry to say, today's litre bikes are hard to beat even with the new ZX14s and Hayabusas.
I use to race my 2001 Hayabusa that made only 165hp geared -1/+1 Vs. 2002 GSXR1K that made 158hp geared -1/-2. Friend was 215lbs suited and I weighed 230lbs suited. From 1st gear to 5th gear it was neck and neck with him slightly ahead by a tire then I would pull through 6th. 2nd gear to 6th neck and neck and I pull slightly at top of 5th then pull harder in 6th. Qtr mile I would have him by .20 with trap speed about the same. I fight the crappy Busa clutch as he fights the wheelie issues. My 60ft was about a tenth better on average. IMO, the 05-06 GSXR1Ks are very quick and pose the biggest threats of all the litre bikes. I believe Suzuki truly did it right with those model years. The new ones just don't have the midrange grunt and pull a lot higher rpm for peak power #s.