This is a half-baked thought:
In three games, by my quick count, we've had 7 drives of longer than 4 minutes -- 3 vs Temple, 1 vs Michigan, 3 vs Purdue. We're in the red on Time of Possession -- +4 minutes vs. Temple and +3 minutes vs Purdue, but - 8 vs. Michigan. This means the defense is out on the field a lot and getting worn out. Better ball control drives -- meaning not asking Tommy to throw first and chewing clock on the ground -- would be key to helping the defense while it sorts out schemes, leadership, identity, etc. All this confusion and underperformance is to be expected from a defense that lost three top filght leaders; the question is how best to make the transition to a new identity. I say, offensive playcalling is the key. Don't ask Tommy to be Aaron Rodgers when he's Joe Flacco.
I know this depends on the ground game asserting itself, and it involves "opponent is loading the box" challenges, but, after three games, I am not left with a sense that Kelly is committed to trying to establish a ground game; it seems much more that he's only too happy to have Tommy throw.