A running QB with decent passing stats is a real weapon in this game. Your perspective on how it should work is just incorrect. The defense is able to stop the QB run if it wants to commit to it, like in real life, but the cost can be high. Have you ever tried passing when the defense uses a spy? It becomes a lot easier and that is the point. If you want a game where RG3 should be able to run no matter what the defense does then just play the CPU on the easiest setting. Otherwise abuse the spy then when they are forced to stop using a spy break off a nice run.