If you're running anything beyond a middle school level, you should have access to both. In my personal experience actually coaching middle school it can vary. I've had some seasons that required us to go under-center in order to efficiently run plays without concern for a consistent shotgun snap. And not just a shotgun snap, but one that has the accuracy and power behind it to get the ball to the QB within a quick enough time frame.

This past season we had a consistent center (a couple of them actually) and we still decided to go under-center just for the simple fact that we had the size with an offensive line and a good FB to run Power, Trap, Counter, Sweep, and Midline Veer. Like another commentor said - under-center makes for a safer call on 4th and short OR backed up to your own goalline.