I think it's safe to assume that the Niners will be in Nickel almost the entire game, but I personally don't see there being a ton of dime where Willis or Bowman would come off the field. Definitely nothing like what the Niners saw against the Packers or even a healthy/semi-functional Lions team. First of all, with the injuries to Edelman and Stallworth they only have 4 WRs on their 53 man roster so throw 5-wides out the window. To go 4 WRs they'd have to take their back (whether that be Ridley/Vereen/Bolden) or Aaron Hernandez off the field in favor of Matthew Slater. Unless they want to abandon their up-tempo offense, or use it only sparingly against the Niners I doubt that they will have both a back or Hernandez off the field for long stretches of time, which would be the case if they went 4-wide and up tempo. Every time the Pats change personnel they give us a chance to do so as well. So I expect them to hit us a single back, 3-wide, 1 TE set on most plays, with the occasional dose of both heavy spread sets of 4-wide equally mixed in with 12 personnel, so there's a chance the base defense will actually see a few snaps. And very unlikely that Willis and Bowman miss a significant or even notable portion of the snaps.
Without trying to make it sound like the Pats are easy to defend in any way, obviously this isn't the case, I think that the defense matches up well with what I expect will be the Pats personnel throughout a good portion of the game - Ridley, Hernandez, Welker, Lloyd and Branch. Hernandez and Welker are the two that present the most problems, mostly Welker as I'm worried about Rogers' ability to contain him after his performance against Amendola and other legitimate slot guys. And while I don't want to take anything away from Hernandez I have faith that Willis will be able to do a fine job in coverage against him. It's usually the taller TEs that give him the most problems. As every single pundit and 9er fan on this earth has already said, the key to winning this game is to harass Brady on every single snap. Aldon Smith needs to have his usually dominant primetime performance and Cowboy and Ray Mac need to drink their muscle milk because if we give Brady a clean pocket he could pick us apart with practice squad players running routes.