49ers' Harbaugh Invites Quarterback Controversy In the N.F.C. title game last season in San Francisco, it sometimes seemed that the 49ers were playing with one hand tied behind their back. They had no deep passing game with their wideouts; they barely had an intermediate one. Alex Smith completed one pass to a wide receiver in an overtime loss to the Giants. Although Smith has played well this season -- before a concussion knocked him out of last week's Rams game and kept him sidelined Monday night -- he may have lost his starting job to Colin Kaepernick, who dazzled in a 32-7 rout against the Bears (and who may be able to offer more dynamic play in the postseason). At least that's what 49ers Coach Jim Harbaugh suggested could happen: "We'll see. Usually tend to go with the guy who's got the hot hand and we've got two quarterbacks that have got a hot hand. Clark Judge of CBSSports.com called Harbaugh's comment a mistake, "an unnecessary distraction for a team that doesn't need it." Pure and simple, Alex Smith should be San Francisco's starter. He won the job in training camp, and he stayed the starter until he got hurt last weekend. Tim Kawakami of MercuryNews.com spoke to some 49ers in the locker room and picked up a different vibe, saying, "Afterward, even the players who have backed Smith the longest and most loyally had to admit that the QB job is a tossup now." SAN FRANCISCO -- Colin Kaepernick played, Alex Smith watched, and at the end of it, nobody in the 49ers locker room could say that the roles should ever be reversed. In every measurable way, this was a 49ers practical and emotional sea-change, all in a three-hour QB explosion. Right now, Kaepernick is scalding -- he completed 16 of 23 pass attempts for 243 yards and two touchdowns, racking up a 133.1 passer rating. It wasn't just about statistics, either. He looked calm, he threw precisely, and he fired a couple of deep passes that looked as if they were fired out of a missile silo. You can practically hear tight end Vernon Davis gushing, via Kawakami: "I was just so proud of him at that moment, because the ball that he threw me, it was one of those balls that you see Tom Brady throw. Second window, right on the money, wow, surprise. Extra point Smith had been on a remarkable run of his own in the two games before his concussion: 25 for 27 for 304 yards, 4 touchdowns with no interceptions. Should Harbaugh have stuck to the traditional script and declared that Smith would be his starter when healthy enough to return?