The Niners and the Giants have solid 'D's but the Niners have a better running game. Rain and wind are coming to the Bay Area which may make the QB issue/passing game of lesser import. Also, remember how the Niners 'D' handled Drew Brees who was the toast of NFL until last Saturday.
The Pats haven't beat a team with a winning record this year. I foresee Niners v. Ravens on Super Bowl Sunday, both have good defense and the Niners have head coach who seems to be the Second Coming of Bill Walsh.
Alex Smith has brought the Niners back at least five times this year in the fourth quarter - he may not be Joe Montana or Steve Young, but he's a six year vet who is respected by a team that won't quite and most importantly they believe in him.