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Keeping Colin Kaepernick over Alex Smith was still the right choice for the 49ers

At 6-4, after consecutive losses to the Carolina Panthers and New Orleans Saints, some people are beginning to question the San Francisco 49ers' decision to stick with Colin Kaepernick over Alex Smith.

Don't be one of those people.

Jim Harbaugh made the correct choice at the game's most vital position.

Sure, Kaepernick has only two games with over 200 yards passing this season, and his statistics are down across the board. But just because Smith's Kansas City Chiefs are 9-1 doesn't mean San Francisco would have been better off with the first overall pick in the 2005 draft still running the show.

Here's a comparison of each quarterback's stats heading into Week 12:

Smith's numbers are down as well, but he's essentially been the same game-managing, minimal-mistake, checkdown-predicated quarterback he was in San Francisco in 2011 and 2012. 

Taking those statistics to the graduated, Pro Football Focus level, this is how the two signal-callers compare:

(*Accuracy Percentage "accounts for dropped passes, throw aways, spiked balls, batted passes, and passes where the quarterback was hit while they threw the ball – factors that hurt the quarterback's completion percentage but don't help show how accurate they are.")

While those figures clearly point to Smith as the more accurate quarterback, there's a reason his percentages are much higher than Kaep's.

Also per PFF, Kaepernick's average depth of target is 10.1 yards, the fourth-highest figure in the NFL. Meanwhile, Smith's average depth of target is 6.5 yards, the lowest figure in the NFL.

As is the case with just about every "non-elite" quarterback, both Smith and Kaepernick have been the product of their environments this season.

The two are living, breathing examples of Mike Tanier's Rule of Interconnectivity (the first rule). Since reading that rule, I've realized it could be worked in to just about every column I write.

"The quarterback depends on his line. The receivers depend on the quarterback. The defense depends on the offense to not keep giving opponents the ball at midfield. Everything depends on the opponent, so AFC West numbers come with a different set of problems than NFC West numbers. In baseball, the pitcher and batter enjoy a degree of isolation from teammate effects. In football, about the only person who works in isolation is the kickoff specialist."

San Francisco, as a whole, simply hasn't been as good as it was a season ago, and there are obvious reasons why.

No Michael Crabtree. A suspended Aldon Smith. No Mario Manningham. No Delanie Walker. No Dashon Goldson. All, maybe except Manningham, were integral facets of the 49ers winning 11 games in the regular season and finishing a play short of winning the Super Bowl.

Surprisingly, San Francisco's offensive line in front of Kaep' has regressed, as well.

Last year, it was by far PFF's highest-rated run-blocking unit with an average grade in that category of +7.91 per game. This year, that average has plummeted to 1.22 per game.

Frank Gore's numbers tell that story.

As a pass-blocking unit, Joe Staley and Co. averaged a +1.73 grade per game in 2012. This year, they average a score of +0.32 per outing.

Is Kaepernick to blame for some of the regression we've witnessed from the once totally dominant 49ers?

Absolutely.

He's the quarterback and has inarguably taken a step back both as a passer and a runner.

But his powerful arm and gazelle-like speed provide the 49ers with tremendous offensive creativity and raise the team's overall ceiling. While Smith has proven to be a disciplined system quarterback, he's someone who won't single-handedly lose many games but won't single-handedly win many, either.

The 49ers are in "win-now" mode; however, that doesn't mean they're bound to tank if they don't win the upcoming Super Bowl. With the youthful Harbaugh calling the shots and GM Trent Baalke compiling an assortment of additional draft picks every year, San Francisco is visibly focused on remaining viable for many years and believes in the future just as much as it believes in the present.

At this point in his career, there was only so much San Francisco could do as an offense with Smith at the helm. Though he's not exactly over the hill at 29, Kaepernick is three years younger and has started only 17 games and thrown fewer than 500 passes in his professional career.

He's still at the early stages of his development.

With some of the 49ers key players set to return on both sides of the football over the next few weeks, don't be surprised if Kaepernick shows similar flashes to what he displayed a season ago and his team makes another deep voyage into the postseason.

San Francisco's front office made the right choice to stand behind Colin Kaepernick as its starting quarterback.

Don't let anyone tell you any different.  

Brad Gagnon

About Brad Gagnon

Brad Gagnon has been passionate about both sports and mass media since he was in diapers -- a passion that won't die until he's in them again. Based in Toronto, he's worked as a national NFL blog editor at theScore.com (covering Super Bowls XLIV, XLV and XLVI), a producer and writer at theScore Television Network and a host, reporter and play-by-play voice at Rogers TV. His work has also appeared at Deadspin, FoxSports.com, The Guardian, The Hockey News and elsewhere at Bloguin, but his day gig has him covering all things NFC East for Bleacher Report.

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