I should have paid a little more attention to the defensive formations the Seahawks have in place on plays where they get beat by a RB straight up the gut. Also the offensive formations.
I am pretty sure the Niners were at least running a TE and FB (sometimes 2 TE's) on the plays where they pounded it up the middle with Frank Gore. When you see two tight-ends and a full back, you know it will probably be coming right up your a$$. So the defensive play calling should drop Chancellor in to have 8 men in the box. If the play isn't called like that, then Bobby Wagner should audible the D. One thing I rarely see is Wagner adjusting coverage. Tatupu was good at that, reading defense and adjusting the coverage accordingly. Wagner is a rookie, so he is just running the plays exactly how Bradley calls them. I don't think Bobby wants to piss Bradley off by adjusting the play on the field and end up making a big mistake that leaves someone wide open.
Not sure what people think of Gus Bradley. But I think he's an average to fairly good play caller, usually, against the right offenses. While Bobby Wagner is a skilled player, physically and mentally he can read plays. But I don't think he's quick enough to read the defense then adjust all the players on the defense accordingly. I really only see him calling in one of the safeties to blitz (Thomas when he thinks its going to be a pass play and Chancellor when he thinks they're going to run it) and i've seen him call out to KJ Wright on a few plays. Don't think i've seen him run up and adjust the D-line and definitely haven't seen him move LeRoy Hill anywhere. But I think that's because Hill is a seasoned veteran while Wagner is a rookie. He may be hesitant to tell Hill where to go and what to do.