Another issue is the sheer amount of time it takes to get a play off. These time outs the Niners take in the first quarter because the play call has not been there has been a problem for what seems like an eternity. Damn near every other team in the NFL can get a play call in with plenty of time to make adjustments. The Niners cannot. This also destroys the Niners in the two minute drill. I also think this is limiting what Kaep can do with the offense. He's far to concerned with getting all the adjustments just right in a limited amount of time because the play call gets in with just about 9 seconds left to get the play off.
That is on Roman and Harbaugh. And quite frankly I think it is on Roman more than Harbaugh.
Again, Roman will be gone at the end of the season if not before then. This offense has had problems since he's been here and it hasn't gotten better. QBs have changed, but the overall issues with it have remained.