If you go too large on port sizes, then (particuarly when not on boost) when the engine is at low rpm, the gas speeds travelling down the ports will be lower, which leads to less flow towards the end of the intake stroke, when you are relying on te gas coming in having momentum (as the vacuum in the cylinder is no longer as great) and also when the piston starts to come back up if you have high enough gas speeds heading towards it then it stops reversion of the gasses.
Most good aftermarket heads will therefore NOT go for massive ports, but will instead concentrate on the shape of the ports, and particuarly the valve throat, where gains can be made in flow (by removing restrictions) without having to increase diameter and lead to a drop in gas speed.