As most know, the controversy was ignited by Kaepernick's brilliant performance in the 49ers' dominant 32-7 victory over the Chicago Bears on Monday night. Already a fan favorite, that performance ingratiated Kaepernick with the San Francisco crowd even more while impressing head coach Jim Harbaugh.
When asked who would be getting the start in Week 12 against the New Orleans Saints, Harbaugh replied with a rather coy answer.
"I usually tend to go with the guy that has the hot hand and we have two quarterbacks that have a hot hand," Harbaugh said (per ESPN).
It doesn't take a nuclear physicist to figure out that the 49ers head coach is at least thinking about making a change. And all things considered, it's an understandable (but wrong) consideration.
It's rather apparent that San Francisco sees Kaepernick as the quarterback of the future. The team traded up to take him in the 2011 draft and has weaved him into the offense for rushing situations all season.
There's also no denying that Kaepernick was sensational against the Bears. Facing off against far and away the NFL's best defense, according to Football Outsiders, the second-year quarterback went 16-of-23 passing for 243 yards and two touchdowns without an interception.
For a guy who was mostly used in rushing situations as a pro, he looked like a comfortable veteran in the pocket. Kaepernick checked down when necessary, displayed beautiful accuracy on his throws and showed off powerful arm strength.
Plus, as we have seen with Andrew Luck and Robert Griffin III this season and Cam Newton last season, you no longer have to treat young quarterbacks with kid gloves. The offensive changes in both the NFL and college have made the transition infinitely easier than it used to be, so there's little reason to think the youngster would completely fail.
That's all forgetting one thing: Smith has been nothing short of fantastic this season. The incumbent starter has completed 70 percent of his passes this year for 1,731 yards and 13 touchdowns against five interceptions, putting Smith into a position to set a cavalcade of career highs statistically.
Smith's performance also carries weight in the advanced metrics community. ESPN's QBR rates Smith at 69.8, which is ninth-best in the NFL, and Football Outsiders' DVOA (Defense-adjusted Value Over Average) has him ranked seventh in the league thus far.
The 49ers' decision has Super Bowl implications, all of which point to Smith being the better answer.
Though Kaepernick is 25 years old, he is just in his second NFL season. Only two quarterbacks (three if you count Kurt Warner) in league history, Tom Brady and Ben Roethlisberger, have been the starter for a Super Bowl winner in their second season.
Let's also not forget that this was one game and Smith was actually expected to play for most of the week. Had the Bears known that Kaepernick was the quarterback from the get-go, it's undeniable that there would have been some game plan changes.
If Harbaugh makes the change based on the Chicago game and it backfires, he's submarined the entire 2012 season. Smith certainly wouldn't be happy considering his level of play and many would be baffled about the decision to tinker with a winning formula.
This season isn't about building for the future. The window in the NFL for championships is so unbelievably short that the 49ers need to capitalize on theirs before it vanishes.
All of this boils down to who gives the 49ers the best chance to win the Super Bowl. Despite Kaepernick's brilliance last week, the answer to that question is Smith.
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