When you make the ports larger you also decrease the velocity of the gasses that pass through them and decrease the crankcase compression. This has to be taken into consideration and compensated for - depending on the application the motor will be used for. Many times I port engines by using epoxy to make passages smaller to increase the velocity of the gasses traveling through them. Epoxy can be used to correct dips, valleys and other casting flaws and reshape poorly designed transfer port passages. Though porting increases the chances of fuel entering the cylinder at the right time all the parameters of the engine must be worked out ahead of time.
Careful planning can produce the desired effect.
It is most important to plan exactly what the engine is going to be used for and what its targeted rpm range is going to be. I guess I'll fall under the ETC. category. Typically they are enlarged considerably from stock. I know that on 250R cylinders that's the easiest and first place to head to open up a cylinder. Backcountry Damn premium response, Rick.