Yeah, most bikes (and cars) are running leaner than ideal for power to meet EPA regs. Even modern-design liquid cooled bikes like mine with fuel injection are still running way leaner at some rpms than is ideal.
But the restrictive pipes and air cleaner are more to meet the noise regs, aren't they? You can probably leave the bike stock except for rejetting and improve drivability a lot and improve peak power a little. But for serious power gains you need more flow - pipes, air cleaner, maybe cams (which were also chosen with pollution in mind, no doubt).
"Yeah, most bikes (and cars) are running leaner than ideal for power to meet EPA regs."
Not true for cars. There are no emissions limits that need to be met at wide-open-throttle, so there is nothing to "hold back" when the pedal is floored.
Also, if the mixture is too lean, NOx emissions go up, which the EPA also frowns upon.