San Francisco 49ers: Decision to Start Kaepernick over Alex Smith Will Backfire

Ethan DemersContributor IINovember 25, 2012

SAN FRANCISCO, CA - NOVEMBER 19: Colin Kaepernick #7 of the San Francisco 49ers runs onto the field for their game against the Chicago Bears at Candlestick Park on November 19, 2012 in San Francisco, California.  (Photo by Ezra Shaw/Getty Images)
Ezra Shaw/Getty Images

Ten games into the NFL season, Alex Smith ranks fifth in quarterback rating (104.1), first in completion percentage (70.0 percent), fourth in yards per attempt (7.98) and is tied for 27th in interceptions (5).  Now here’s the strange part—he’s being benched for Colin Kaepernick, a second-year quarterback who has started just one game in his short NFL career.

Although Jim Harbaugh refused to publicly name a starter during his press conference on Friday, the 49ers are planning on starting Kaepernick Sunday in New Orleans (via Sports Illustrated's Jim Trotter). Kaepernick has been getting the first-team reps in practice all week.

In his Monday night start against the Bears, Kaepernick went 16-of-23 for 243 yards, two touchdowns and a passer rating of 133.1. In relief of Smith against the Rams in Week 10, Kaapernick went 11-of-17 for 117 yards. While those are undeniably impressive stats for someone as inexperienced as Kaepernick, it’s still extremely surprising to me that the 49ers are choosing to go with Kaepernick in New Orleans.

Before Jim Harbaugh was hired as the 49ers head coach prior to the 2011 season, Alex Smith had endured an extremely disappointing career. Originally the No. 1 overall pick in the 2005 NFL draft, Smith played under six different offensive coordinators in his first six seasons in the league.

When Harbaugh arrived and the lockout ended, Smith signed a one-year, $5 million contract with the 49ers. Prior to the 2011 season, Smith had never finished a season with a higher passer rating than 82.1. Yet Harbaugh still believed in Smith enough to encourage the 49ers front office to re-sign him after his disastrous first six seasons in the league.

Since Harbaugh has taken over as head coach, Smith is 20-5-1 as a starter. There are those who have said that Harbaugh has made Alex Smith, but however you look at it, he’s been a successful and efficient starter in the last two years.

Often times in the NFL words like “efficient” and “game manager” carry almost negative connotations. For example, most people supporting Harbaugh’s decision to go with Kaepernick this week will probably cite the opinion that Alex Smith is a game manager, but not a quarterback that really threatens defenses.

The reason I don’t like the term "game manager" is because of its ambiguity. Apparently Smith is one because of the relatively low number of interceptions he’s thrown in the last two seasons (10). Those that are applying this cliché tag to Smith haven’t really done their research, however.

In what way is a quarterback that ranks fifth in passer rating and fourth in yards per attempt only an effective game manager? That’s called being an effective, if not an elite, quarterback.

Smith might not throw for as many yards or touchdowns as some other quarterbacks, but that’s a result of the fact that the 49ers have a great defense and running game; their offense is first in the league in rushing and their defense ranks first in the league in points allowed per game. Since the 49ers run the ball so often—they’ve run the ball the second most in the league—and are usually playing with a lead, Smith isn’t asked to throw the ball as often as many other quarterbacks.

Last offseason the 49ers were pursuing Peyton Manning, and Smith wasn’t too happy about it. How could he be? He had finally found success with a coach that seemed to trust him and his job still didn’t seem secure. In the end, Smith stayed in San Francisco and signed a three-year contract with the 49ers and Manning went to Denver, but that doesn’t mean Smith forgot what happened.

Smith told Matt Barrows of The Sacramento Bee that the 49ers' involvement in the Manning sweepstakes in March was "a little awkward":

“Certainly there are a lot of forms of motivation," said Smith after Manning agreed to terms with the Denver Broncos. "I guess that's there a little bit as far as motivation."

What this demonstrates is that Smith was already a little insecure about his job security heading into the season. If Smith needed to be reassured by Harbaugh that he was their guy in the offseason, then it seems doubtful that he will take Harbaugh’s decision to start Kaepernick over him well.

In starting Colin Kaepernick, Jim Harbaugh could be losing Alex Smith forever. Harbaugh was the first coach in years that seemed to truly believe in him, but one would think their relationship must be somewhat fractured at this point.

When I first heard Harbaugh ambiguously say after the game that they would have to go with the “hot hand” going forward, I thought he blew an opportunity right off the bat to not let this story gain momentum. While he could have kept the trust of his former starting quarterback, Harbaugh instead chose to spark a media circus around an unnecessary quarterback controversy.

As surprised as I was, I figured Harbaugh was just trying to keep a competitive advantage over the Saints by not disclosing who the starting quarterback would be. I was wrong, and Harbaugh is serious about starting Kaepernick.

If I were a 49ers fan, my No. 1 fear would be Kaepernick struggling and Alex Smith not having the confidence to play well if called upon. It might not happen against a weak pass defense like the Saints this week, but I would be surprised if it didn’t happen eventually this season.

Considering the short leash that Smith was on, I would expect Kaepernick to be on a similarly short leash. If Smith is asked to play in relief of Kaepernick, will he be able to just shrug off the pressure to perform above and beyond the expectations that have been put on him by Harbaugh? I doubt it.

Above all, Harbaugh’s decision to start Kaepernick is bad for team morale. What it really says is that if you’re a starter and you get injured, be aware that you may be replaced if the backup does reasonably well. That’s no way to manage a football team. I’m a little surprised that the 49ers’ locker room hasn’t rallied publicly behind Alex Smith, but I’m sure they’ve already done so privately.

If the 49ers fail to make the Super Bowl, then don’t be surprised if people look back to the decision to start Colin Kaepernick in Week 12 as the primary reason why.