on most engines, if you take a look at the stock intake port compared to the engine port, the intake manifold port is round, about the size of a dime, while the engine port is semi-square, and twice the size. obviously, shaping the manifold port to match the engine would allow for a better flow of the fuel mixture.
while you're looking at the intake manifold, if you look inside, mostly at the bend, you can see a lot of burrs/casting flash, which should also be removed.
keep in mind that the intake manifold doesn't always have enough metal to match the port perfectly, and if you go to far you can compromise it's strength.
a motor that breathes better will run faster and smoother. it's the easiest (and cheapest) way to squeeze all the power possible out of these little bastard$...