I don't often predict specific games. But I think that the 49ers have a set of unique weaknesses that Belichick's team can exploit.
a) They play their defensive starters the whole game. All 10 of 11 defensive starters are averaging 95% of the snaps and even more. That makes them susceptible to the wearing effects of the speedy no-huddle.
b) Their pass rush is very unbalanced. It comes from only four players,withan outsized amount from only Aldon Smith.
Aldon Smith, OLB 19.5 sacks
Ahmed Brooks, OLB 5.5 sacks
Justin Smith, DE 3 sacks
Novaro Bowman LB 2 sacks
c) They decided that Alex Smith won't take them all the way, so they are playing an inexperieced rookie QB, after they thought they safely clinched a Playoff berth and bye.
d) The losses that the 49ers had were to teams that ran the ball right at them, and completed short passes against them.
e) Their Defense is a 3-4 one gapping Defense like the Steelers, Texans and Ravens play.
Belichick has always found a way to take the oppositions best player away. Expect another JJ Watt episode. Belichick has built a team that specializes in the run and the short pass along with the no huddle as a means of wearing out the opposition in the second half; and as important, negating the pass rush.
Belichick teams have had mixed resullts playing against rookie QBs, UNLESS he has some film of the rookie. Then the results are disasterous for the inexperienced QB. Kaepernick has started enough for their to be some film of his tendencies.
Finally, Belichick's teams have seldom had problems playing against a one gapping 3-4, provided his team has a semblance of a running game.
Add in the MVP QB play of Tom Brady. Then consider that the overload 49ers post against the OLT and OLG with the Smith duo is their basis for all their pass rush. Seldom do they run across a pair of strengths like Nate Solder and Logan Mankins. All of this adds up to the high probability of a mismatch in favor of the Pats.
OTOH, the 49ers amazingly resemble the Ravens. They possess a great pass rusher Aldon Smith, equivalent to Terance Suggs, a great MLB Patrick Willis, equivalent to Ray Lewis, and a heady Safety, Dashon Goldson, almost equivalent to Ed Reed. They even have a great RB Frank Gore, their equivalent to Ray Rice. They don't seem to have a Ngata or a experienced QB like Flacco. Sopoaga and rookie Colin Kaepernick are but pale imitations. But Whitner is a good SS.
Baltimore has given the Pats headaches but usually lose, although not this year.