One of the most surprising and intriguing storylines of the last few weeks of the NFL season has been the quarterback situation in San Francisco. The unspoken rule in the league is that a player isn’t supposed to lose his starting role because of injury. When Alex Smith suffered a mild concussion, though, Colin Kaepernick was so good in relief that he was named starter even once Alex Smith was declared healthy. This has created all sorts of controversy in the media and all sorts of challenges for handicappers. Here is a look at seven different factors to consider when determining how you are going to deal with this high-profile and relatively-unique quarterback controversy:
 
Perception differs from reality of Smith

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A lot of people seem to have the impression that this is a clear-cut decision — that starting Kaepernick is a no-brainer. The only way you can really think that, though, is if you haven’t adjusted your perception of Smith to your new reality. This year Smith has been efficient and effective. He has completed 70 percent of his passes, and his 7.98 yards per attempt is very solid. I’m not saying that coach Harbaugh has made a bad decision here, but it’s very important for bettors to compare the two quarterbacks based on reality, not outdated perception.

Kaepernick hasn’t come from nowhere

As ridiculous and frustrating as the misperceptions about Smith are the ideas that people seem to have that Kaepernick is an overnight success story. You could think that if you don’t pay attention to college football, but his talent is no surprise. Playing at Nevada, Kaepernick became the only FBS QB ever to pass for 10,000 yards and run for 4,000 in a career and the first to pass for at least 2,000 and run for at least 1,000 in three straight seasons. In his senior year he was a counselor at the Manning Passing Academy, and he wowed people with his mobility and his arm. In other words, this is no fluke — this is a very good quarterback getting his chance. It would be as much of a mistake to discount Kaepernick as it is to discount Smith. What makes this situation so challenging is that both guys are quality options.

Public definitely favors Kaepernick

Smith is methodical. He’s efficient, but he’s not flashy. Kaepernick has a bigger arm and faster legs. NFL fans are pass-crazy right now, so it’s no surprise that they are favoring Kaepernick — especially given the story of his emergence. Bettors need to be aware of public perception and what impact that will have on how lines are set and how they move — both when Kaepernick is starting, and if Smith were to take over again for some reason.

Offense isn’t primary focus for the Niners

The impact of this situation won’t have as much impact on public perception, and therefore on the lines, as it would for other teams. The Patriots or Saints, for example, are known primarily for their offensive firepower and their star quarterbacks at the helm of those offenses, so a situation like this would impact the foundation of how those teams are seen, and the public would react very strongly. The Niners, though, are seen as more of a strong defensive team with a good running attack than an offensively-dominant squad. They win by shutting teams down, not overpowering them on offense. The impact of which quarterback they choose, then, is far less than it could be.

Receivers complement Kaepernick

One area where Kaepernick has a distinct edge over Smith is in arm strength. He’s got a cannon. In the offseason the Niners invested heavily in their receiving corps, adding three deep threats in Randy Moss, A.J. Jenkins, and Mario Manningham. Kaepernick is better positioned to maximize the impact of those additions than Smith is, so the longer he plays, the more likely we will see a significant boost inn wide receiver productivity.

Doesn’t really matter the next two weeks

If the Niners are the team we think they are, then it really shouldn’t matter too much who is taking snaps over the next two weeks. They face St. Louis this week and Miami next week. They have the ability to make life very difficult for both starting quarterbacks in those games, and they have enough ways to exploit either defense regardless of who is playing. In other words, they should win those games if they play at their potential no matter who starts. The same goes for their final game — a home contest against Arizona. The true impact of this quarterback controversy will really only be felt in two games — trips to New England and Seattle in Weeks 15 and 16.

Only becomes a major issue when things go poorly

The media and the public seem to be making a big issue of this situation right now. To me it’s only really interesting once things go poorly. The team is talented enough, and defensively sound enough, that either guy is more than capable when things go well. It’s when they face adversity that we’ll really face a handicapping challenge, though? If Kaepernick falters will the public desert him? Will his teammates? What happens if Smith quits acting like a good teammate? How about if a QB turns a win into a loss? Until that happens this controversy isn’t particularly controversial or relevant for bettors in my mind.