For me, this THIS is the biggest difference.
He looks hesitant to throw sitting in the pocket.
He looks hesitant to run even when it's open, almost like he's been told not to.
No question on his arm talent, it's absolutely there. But I don't know if it's paralysis by analysis, not trusting his abilities, plays not playing to his strengths, etc., but he isn't playing like a QB who believes in himself and/or his teammates.
I also don't think his issues with scrambling/extending plays are an athleticism thing. He's not the athlete Haarberg is, but he's plenty athletic to scramble for a few yards and maybe break a big one in the right circumstance. To me, the reason he looks slow is he's not decisive about it. It looks like he's desperately looking to throw the ball until the millisecond he crosses the LOS.
I was impressed he put his body on the line on the play he got hurt, but the reason he got hurt was because he was hesitant in committing to it, and then didn't have a good feel for how to take the contact. Probably because he barely practices those situations would be my guess.
It really just LOOKS like he's been told not to run with the way he acts/reacts.