Motorcycle engine design is a compromise. Bore and stroke may decide a large part of an engine's character, but the fixed nature of the other components is equally relevant – camshaft profiles work best at specific engine speeds, as do the size and shape of the inlet tracts, combustion chambers, valves and exhaust. Designing them for high revs and power can mean sacrifices lower in the rev range, and turning for low-rev torque makes things wheezy at the top end.
There will also be compromises paid in emissions, economy and response away from the region where intake, cams and exhaust give optimum performance.
The ideal solution would be an engine with variable geometry. Unfortunately the theory is sound but the application is still a few years away, which is why technology like variable valve timing has been tried but mostly rejected. Too much complication and cost, too little reward. Honda's VTEC switches between two and four valves per cylinder based on revs, but isn't really variable as valve lift and duration is unchanged. Yamaha's YCC-1 system on the R6 and R1 alters inlet trumpet length but, with two preset positions, isn't a truly variable technology that has advanced motorcycle design.
Except, that is, for Yamaha's EXUP. A simple throttle valve located in the exhaust pipe, the concept has proved so successful that every major motorcycle manufacturer now fits them.