In Week 11 against the Chicago Bears, San Francisco 49ers head coach Jim Harbaugh had no choice but to start Colin Kaepernick. With starting quarterback Alex Smith out with a concussion, the backup was inserted into the starting lineup, and led the 49ers on an offensive rout of the vaunted Chicago Bears defense.

Now, Smith is healthy, and Harbaugh is set to make a decision on a permanent starter going forward. After Kaepernick was given the start against the New Orleans Saints on Sunday, the second-year player is expected to remain under center.

Harbaugh’s decision to bench a healthy Smith may be a controversial one. Which quarterback deserves to be the 49ers starter?

Smith didn’t do anything to lose his job. Last year, he was the starter of a team that came within an overtime loss of reaching the Super Bowl. Through the first half of the 2012 season, Smith and San Francisco looked to be on their way to another deep playoff run.

San Francisco even had a few great offensive performances with Smith at the helm. The 49ers had three games with at least 30 points, with Smith making some impressive throws. He’s even fifth in the NFL with a 104.1 passer rating.

Even with the 49ers success, there have been questions about whether or not Smith can be the main catalyst for winning games. In the past two seasons, he’s become a master of not making mistakes, throwing just 10 interceptions. Smith has done just enough to win, behind a great defense and a very good running game.

In Kaepernick’s two starts, he’s shown a playmaking ability that Smith hasn’t shown in eight years with the 49ers. In a league where quarterbacks can throw the ball with more ease than ever, Smith has only one 300-yard game this year, and threw for barely over 3,000 yards last season. Kaepernick threw for at least 231 yards in his two starts. Smith only reached 232 passing yards twice this season.

Kaepernick also brings another dimension to the 49ers offense with his ability to run. Even when Smith was the starter, Kaepernick was used similarly to Tim Tebow, playing in wildcat packages and giving opposing defenses different looks. With him on the field at all times, defenses will constantly be on their toes.

It’s no surprise that Kaepernick will likely lead San Francisco into the playoffs. He was drafted by Harbaugh. The head coach inherited Smith, a perceived draft bust before last season.

Going 19-5-1 in one and a half seasons certainly doesn’t warrant losing a starting job. However, Kaepernick may be just what the 49ers need to get over the hump.

In last season’s NFC Championship Game, the 49ers lost in overtime, unable to score more than 17 points. Smith was unable to get much going on offense, completing just one pass to a wide receiver. When the 49ers face a top defense in the postseason, Smith’s limitations could prevent San Francisco from reaching the Super Bowl.

It’s unknown what Kaepernick will do under the bright lights of the playoffs. There’s a chance that the moment will be too big for him, and these past two games might just be a fluke. It’s also possible that he is what San Francisco was missing last year, and is exactly what the 49ers need to go all the way.