It all has to do with gas velocities, inertia, and scaveging.
Air does not just flow through the intake or exhaust, it flows in pulses. Inertia of the gasses helps scaveging and cylinder filling.
Here's a quick explanation:
At low rpms, you need high gas velocities so that the gas has a bit of inertia to fill the cylinder better on the intake stroke. You also need high exhaust gas velocities so that the inertia of the gas will help "pull" the gas out, like siphoning (also the pulse will help pull the next pulse out, but this has to do with header design).
At high rpms, gas velocities are already high, so port sizes can be larger. Same principles apply, but since the gas is already traveling so fast, the ports need to be big enough so that there is no pressure drop due to a restriction.
The rule of thumb is that a long, small intake/exhaust tube will boost low end power because the gasses will have a higher velocity (thus, higher inertia). Smaller exhaust ports will also promote better scaveging, thus increasing power at lower rpms. Problem is, trying to run small ports at high rpms. The tubing can't support the flow, so you end up choking the engine at high rpms. Now, short, large intake/exhaust tubing promotes better top end power because the tubing can support the higher flow.
So, there is a compromise to be made...make the tubing for low end power or high end, etc. etc.
Header design also plays a role in exhaust performance.
So, now look at Honda's intake design. When the butterflies are closed at low rpms, the intake is a small, long length intake, which promotes low end power. When the butterflies open, the intake tubing is essentially larger, and it appears shorter to the engine, so it promotes top end power.
Whew...that's about all I can think of right now. I know I made some typos, but I am too lazy to correct my spelling!
North Texas Prelude Owners Group