Because Nintendo was too cheap for two analog sticks. When analog sticks came out there was a bit of a problem. How do you add an analog stick and keep the d-pad? Sony chose to use two, added underneath, which works but then you need not one but two sticks. Sega chose to simply put a stick on the left side, which means you can use the d-pad or the stick but not both at the same time, and looks asymmetrical. Nintendo chose to be different and put the stick in the middle. That way you can use the analog stick and d-pad, analog stick and c-buttons, or d-pad and c-buttons. It's a lot less awkward than you might think, but it looks strange, makes the controller huge, and makes portabilizing the thing a bit harder.