One potential reason: Kaepernick's ability to turn negative plays into positive ones.
2012 Niners QBs Under Duress
Kaepernick and former starter Alex Smith have been under duress a similar number of times this season, even though Smith has 2.5 times as many action plays. That is because Kaepernick has held the ball 4.1 seconds following the snap on average, the highest figure in the NFL. Smith has held the ball 3.4 seconds, right at the league average.
The extra time Kaepernick holds the ball leads to more snaps under duress. ESPN defines duress as when quarterbacks throw or scramble after being forced from the pocket, or when a defender has a clear path in the quarterback's line of sight, or when the quarterback has to alter his regular throwing motion or is forced to move within the pocket due to pressure.
Kaepernick averages 8.0 yards per pass attempt in these situations. Smith averages 1.2 yards per attempt. Those numbers, courtesy of ESPN Stats & Information's John McTigue, translate to a significant advantage for the 49ers if Kaepernick can sustain them.
Smith ranks third behind Tom Brady and Peyton Manning in Total QBR (79.2) and seventh in NFL passer rating (101.8) when he delivers the ball within 3.4 seconds. He ranks only 19th in QBR (26.7) on the other plays largely because he has taken 21 sacks on them. He ranks third in passer rating (113.7) for these situations because sacks don't count in the calculations.
Sacks very much count during games, of course. Smith has taken more of them since the start of the 2011 season (68) than every player but Aaron Rodgers (73), who has 280 additional action plays over that span. Rodgers also has a 73-13 ratio of touchdowns to interceptions during that time (30-10 for Smith).
The NFL is a week-to-week league. An injury or unexpected development could thrust Smith back into the lineup at any time. But if Kaepernick continues on his recent trajectory, it is possible Smith has made his final start in a 49ers uniform.
The team must pay a $7.5 million bonus to Smith if he remains on the roster April 1. Releasing Smith before that date becomes more likely if Kaepernick is the clear-cut starter. Smith has remained with the 49ers in the past when all signs pointed to him leaving. He could conceivably rework his contract and stay in a diminished role. It's premature to write him off as a 49er.
But with Kaepernick getting the call for a third consecutive week and the second time when Smith was cleared to return from a concussion, it's clear the 49ers think Kaepernick can become their long-term starter now. They traded up in the second round of 2011 draft to get him, a strong indication Harbaugh thought the team could build around his skills. The 49ers have subsequently invested early draft choices in receiver A.J. Jenkins and running back LaMichael James, but neither has played.
Harbaugh made what had to be an uncomfortable decision given all Smith has come to represent. There is certainly risk associated with benching a quarterback with a 19-5-1 starting record. But the team would not be making this move, in my view, without feeling strongly that Kaepernick represented a significant upgrade. That could make a painful choice a clear one, at least internally.
As the head coach, Harbaugh needed to put the team first in any decision he made at quarterback. He didn't owe anything more than honesty to Smith. He might have cast himself as an "Alex Smith guy" when it served the team, but he has to be a 49ers guy first, no matter what. So, if Kaepernick indeed represents a significant upgrade, the 49ers needed to make the change.
In this case, however, the move also meant sending an unfortunate message regarding concussion disclosure. Had Smith not reported the blurred vision he suffered against St. Louis in Week 10, there's a chance he might have remained in the lineup, preventing Kaepernick from seizing the starting job. Even if Smith could not have kept playing, any player watching from the outside can see the potential short-term costs associated with concussion disclosure.
The events of the past three weeks could end Smith's career as a starting quarterback in the NFL. They could cost him millions of dollars. Smith seems to have his priorities in order. He made the right decision regarding concussion disclosure and probably would act the same way again in the interests of his growing family. He's banked millions already. But what about the less-established player seeking to keep his job for a shot at earning financial security for his family? The message to him is clear.