Kaepernick's involvement raises concerns for both teams

SAN FRANCISCO -- Nobody was complaining about the integration of backup quarterback Colin Kaepernick into the 49ers' offense after strong showings against the New York Jets and Buffalo Bills.But when the first 49ers' drive stalled Sunday against the New York Giants on a play in which running back Frank Gore was stopped for no gain on a handoff from Kaepernick on a zone read option, it raised eyebrows.Does the 49ers' use of Kaepernick as a speciality quarterback in place of starter Alex Smith prevent the offense from establishing a rhythm?"I think that's a concern," 49ers offensive coordinator Greg Roman said. "I think it's always a concern. I think everything is a concern. But, yeah, I think that's something that we've got to be mindful of. Got to really take a look at and try to make the best decision for the team."Kaepernick's play time in significant moments has increased every game. He played four snaps against the Jets and seven against the Bills before entering late in those games for mop-up duty. He played nine snaps against the Giants before taking over for the final series with the game out of hand.The Seattle Seahawks have taken notice, and they expect to see Kaepernick's unique skill set Thursday night at Candlestick Park.The question is, how much will they see?The Seahawks have three games of film to study, but coach Pete Carroll said they also have to figure out how Kaepernick might be used against them. What new wrinkles from the Kaepernick package must the Seahawks be prepared to face?
"We're trying to figure that out," Carroll said. "That's a big challenge in any week, let alone a week that's short. There's a lot of complexities that they do. Fortunately for us, we did just play Carolina and we saw one of the top running quarterbacks (Cam Newton) in the league with an enormous package of run game for the QB."But they've definitely taken Kaepernick's game to a new level, and not just running it, but throwing it as well."