Originally Posted by Martian

Exhaust geometry on bikes is tricky. While greater flow can be helpful, you also need to be mindful of the scavenging effect. Basically, exhaust pulses help to pull spent charge out of the cylinder, increasing performance. If you change the exhaust you can alter and harm the overall effect, thus decreasing performance. I'm not sure on the specifics, since I've never done any real mods on bikes.

The effect also exists for cars, but it tends to be less of a concern, since the numbers are bigger in general.