But, I believe that since I am not tying to "fly" though the air, I am directing the air. How can this be bad? Please explain.
Well, you're not directing air. It's getting sucked in, and you're hoping it goes some place you want.
On the intake side, you want an amount of surface turbulance to keep a boundary layer of mix that will keep the stuff in the middle from "sticking" to the intake walls and becoming liquid.
Additionally, sometimes you want to shoot the air/fuel mix at a particular part of the combustion chamber. Yeah, some wisdom believes that you want it everywhere, but, invariably, it doesn't work that way. Modern combustion chamber shapes usually use the fact that more comes in one way or another to an advantage. Sometimes there's a reason for shrouding a valve. Some times there are reasons for decreasing the intake port size so that the velocity of the intake charge is greater.