On the contrary, most people think he has a very high "football IQ." One of the first compliments generally paid his way is how intelligent he is.
Overall, I see your point, and I think you're dead on with his mechanical inconsistencies. But I think the silver lining is that these can be corrected with good coaching. He had no QB coach his rookie year, so I seriously question how much time he spent going through QB specific drills. One thing I noticed in the game was how quick his back-drop was. Minor, I know. But it leads me to think that some of these mechanical issues were addressed. Lets hope so!!!