There are many possible factors contributing to improved results from the defense including: the emergence of Aldon Smith and Navarro Bowman, excellent play by McDonald, the addition of Whitner as a stabilizing influence in the secondary, etc. etc.
What I would like to focus on here, however, are two things that I think may be quite important this year: 1) the effectiveness of the Nickle defense and 2) the ability to generate pressure with fewer blitzes (e.g., than less year). I think both have allowed a secondary that is perhaps less than stellar to be quite effective as part of a very intelligently designed and executed team defense.
As you all know the advantage of a Nickle is that it is generally a better defense against the pass; the disadvantage is that can be vulnerable to the run. The 49er Nickle, as presently construed, however, includes Bowman and Willis as the ILB's. (Additionally, Goldson hits and supports the run better than average for a free safety). Particularly the former (the presence of Willis and Bowman) makes the the Niner Nickle not easy to run against, thus in the cost-benefit analysis regarding the Nickle, there would seem to be very little cost (except in short yardage situations where and extra big body in the middle is essential).
This enables the team, in my opinion, to use the Nickle more often than would otherwise be the case. This leads to having 5 DB's on the field, for most of the game in some cases, which reduces the pressure on each safety and corner. The excellent coverage ability of Willis (and Bowman), who tends to cover tight ends in man coverage (one-on-on) underneath when required, further reduces the pressure and responsibility that passes to the secondary.
So I guess what I am suggesting is that the excellence of the Willis-Bowman combination has a two part effect in improving the pass defense:
One part is that their strength against the run discourages teams from trying to run at our Nickle, reduces, perhaps dramatically, the incentive for an opposing QB to audible into the run against the Nickle. This enables the niners to use the Nickle in a wide variety of situations, i.e., on many first downs, some 2nd & 4 or even 2nd & 3, etc.
The second is their excellence in coverage, particularly Willis, whose coverage underneath and is an obvious asset. I have heard some suggest that it may be a waste, or misuse, of Willis' talent to have him in coverage so much (when he could be attacking and "hitting"). I would suggest that when we see him in coverage that may be, in a real sense, the second thing he has accomplished on that play. His presence on the field, pre-snap can discourage the other team from running and force them to become somewhat one-dimensional and predictable.
Anyway, that is my 2 cents (or 5 cents). I am looking for a game by game breakdown regarding how frequently the Nickle (or dime) has been used and in what situations (down and distance). (Haven't got it yet.) Any comments or info on that is much appreciated.