Alex Smith has never had a strong arm, nor has he ever had any confidence in his arm. The throw where you need both arm strength and confidence is the one in between the linebacker and the safety. Knowing this, opposing teams could easily gameplan for Smith.
What Nagy has done is schemed completely around this deficiency. Even though teams knew what Alex Smith was incapable of, the offensive system still kept them guessing.
First of all, Nagy installed a ton of pre snap motions from everywhere. This was to confuse the defense and make it easier on Smith to read the defense. I mean, they would have Hunt lined up at WR, motion him back next to Smith in the shotgun, and then motion back to WR. They did a lot of jet sweep motions with Hill pre snap as well. The defense had to try to ignore all of this movement or they were toast.
Secondly, Nagy installed an offense of quick short passes or deep homerun shots, which eliminated the need to try to fit the ball into a window. And this is why they valued speed at WR so much more than anything. He’d have 3 burners all go deep to vacate the entire middle of the field for an easy pass to Kelce. Or he’d call a quick screen pass to Hill while everyone else went deep. And when the defense started cheating to stop these passes, Nagy would go straight for the jugular with deep passes over the entire secondary.
In the times where the play call didn’t work, Smith wouldn’t even attempt to force something else. He’d just put his head down and evacuate the pocket. He’s the prototypical system passer. Most of the credit should go to Nagy on this one.
