This season has seen tremendous variation in the percentage of base vs nickel defense the 49ers use. For example; against the Skins, the 49ers were in base defense for about 32 our of 69 snaps, while against the Lions in week 6, the niners were in base only about 15 out of 83 snaps (and thus played nickel or dime 68 times!). The generous use of base vs the Skins might seem surprising since Washington passed on all but 15 of the offensive snaps. Presumably, however, this choice was part of a game plan to force the opposition to pass, with the sense that Beck would struggle even against the 49ers base defense. This weekend the expectation is quite the opposite I believe.
Because Manning is quite good, and the NY running game has been ineffective, I would expect the niners to employ a great deal of Nickel, even on 1st down. To state the obvious, this gets Culliver on the field to enhance the secondary and Aldon Smith at ROLB to enhance the (4-man) pass rush. Although there may be some blitzing, I think a key to stopping Manning and the Giants is the ability to create pressure with a 4-man rush so that we can maintain a full 7 in coverage most of the time. I would be surprised if Sopoaga plays much more than 15 snaps unless he is subbing at left tackle in the nickel.
The 49ers have an unusual nickel in the sense that both ILBs, Willis and Bowman, stay in. In fact, they play every defensive snap including all nickel and dime. On dime, I think, one OLB comes out and Reggie Smith comes in as a 6th defensive back. The tremendous speed and ability of NaVorro Bowman, and of course Willis, thus lets the 49ers play an unusual scheme.
I do not think that any other team in the NFL (correct me if this is wrong) has ILBs who play every snap or, equivalently, who play in nickel and dime defenses routinely. The excellence of their man coverage underneath is noteable. I also believe that there is no team with more speed at ILB.
The dime has only a 3 man pass rush unless Willis, Bowman, Whitner, Goldson or a corner blitzes. (I think this happens in the dime about 1/3 of the time). To summarize,, I would expect A LOT (80%) of pas defense and very little base. I think the prospect of Manning trying to go deep against base on 1st down is something the 49ers are aware of a will try to avoid. We can probably expect to see a lot of "two - man" defense, in which Goldson and Whitner play zone fairly deep over the middle, and the ILB's and corners provide man coverage underneath (and sometimes further down the field as needed). This will be an important test of the 49er pass defense.
Final thoughts, some have criticized Goldson for his coverage abilities. I think one should also consider that his hitting effects the other teams receivers in ways that do not show up in his stats specifically. Starting with Willis, adding Bowman and two pretty hard hitting safeties, makes going over the middle against the 49ers not exactly a walk in the park. If you do not get crushed, you may get stripped or, what else?