The scheme definitely factors into the defense's problems, but I think personnel decisions are equally at fault. Since Whis has been here, most of the biggest personnel mistakes have been on the defensive side. Each year he's cut one well-paid defensive player who was signed to be a starter the year before (Holt, Laboy, McFadden, probably Porter this year).
Only drafting three starters on D in four years doesn't help, either. Buster Davis was supposed to be the heir apparent to Dansby, even though his physical makeup made him a horrible fit for the 3-4. Cody Brown was drafted to make up for the loss of Berry/Okeafor. Rashad Johnson's lack of development screwed up the Rolle replacement plan. And what was the common thread in most of these FA and draft busts? They made up for their physical limitations with intangibles. That philosophy has blinded Graves/Whis on way too many decisions. Sooner or later, you're bound to start feeling the effects of so many bad moves. Add in an inept defensive coordinator and that process accelerates.
I also think the allocation of resources is kind of skewed. The team sunk tons of money and draft picks into the defensive line and safeties, while the CBs and LBs have mostly been filled with marginal free agents and undrafted rookies.
Getting rid of Davis will help, but the FO desperately needs someone who's better at identifying quality defensive players.