It's like this:
The 49ers defense will do much better against Seattle than anyone else has except maybe the Panthers and Rams. HOWEVER, the 49ers offense will probably screw over their defense again, and in the end it will be just enough to allow the Seahawks to slowly chip away at the 49ers' containment of their offense.
Just like the last game. The only difference will be that the 49ers will have an easier time communicating, which will give them some more points and time of possession.
Due to the game being in San Francisco, the 49ers offense is not likely to give Seattle a free 10 points or so. Their defense will likely hold Seattle to about 17 earned points. The 49ers offense will only get about 13 earned points. Special teams will be even (both teams have outstanding punt coverage), UNLESS LaMichael James muffs another point, in which case the 49ers special teams will give Seattle a touchdown. That's 24 for Seattle, 13 for San Francisco. HOWEVER, the 49ers defense will probably steal one of those touchdowns from Seattle (via a turnover + field position), which will only be converted into a field goal by San Francisco against that stone wall of a defense. Unfortunately for San Francisco, Russell Wilson is bound to make a Bo Jackson in Tecmo Bowl play or two that will lead to a field goal or two.
End result: Seattle 23, San Francisco 16.
Seattle wins if they make the key special teams play. If they don't, I'd have this at about a 19-16 game (OT), going either way. IF, however, Kaepernick doesn't play patient, careful football, he'll make the game losing mistake and this will be 27-16 or 30-16.