You can pin this problem on Bo's overall philosophy of "containing" these mobile QBs.
Bo's idea is to create a containment pocket with his line, to hem this guy in. Don't give him a lane to run, but give him time to pass – the philosophy being that he's less dangerous with his arm than his legs, all the while collapsing that pocket in on him until you get him down.
Where this breaks down is two-fold: First, it is damn-near impossible to play coverage for the four-five seconds this strategy relies on. You have to have two lockdown corners, and we have one (and next year, none). When a WR breaks free, even an unpressured QB for whom throwing is not his primary weapon can find a man to throw to, and make a reasonable throw as he gets open. Even Martinez, before he made his check-down breakthrough, has torched defenses that don’t pressure him.
Second, for this strategy to work you MUST have a superlative pass rush capable of pushing into the QB quickly. We do not have such talent on our D Line. Our guys seem capable of the first prong of Bo's strategy – creating that bubble surrounding him. But we are incapable of collapsing that bubble, nor do we seem capable of maintaining the lanes we must maintain in order to prevent a gap which inevitably allows the mobile QB to break containment and scramble downfield.
What is frustrating is that we do not blitz these QBs. It seems that we're afraid to allow our CBs to play man defense against ANY team we face long enough to get our blitzers to the QB. That is a breakdown either in recruiting or coaching; either way, it falls on Bo.
Our relationship to the blitz is weird. We rarely blitz, and when we do it's into max-protect packages, meaning our blitzers are often picked up, nullifying effectiveness. Blitzing is like playing poker – you gotta know when to hold 'em, know when to fold 'em. Blitzing into max-protect, where the QB has his line and two blockers (either the RB/FB or RB/H-B) is a losing proposition. It is almost always picked up, and we're suddenly vulnerable in the secondary. But on the flip side of that coin, on offense we almost NEVER have max-protect packages in for Martinez. You'd think we'd be able to do some basic self-scouting and see that this doesn't work (on offense) and see that we are pounding our head against a wall when we blitz into these pass-pro packages on defense.
I have no time to go on, but I could go on and on with this. It's a very frustrating situation, on both sides of the ball. What is the most frustrating is that we seem to have no intention of doing anything different, and for a coach that preaches fundamentals and execution, he seems to be ignoring several fundamental aspects of the passing game on both offense and defense.