Did the 49ers make the right choice with Colin Kaepernick?

Colin Kaepernick has posted similar passing numbers as Alex Smith since taking over the job in San Francisco. AP Photo/Matt Dunham

SANTA CLARA, Calif. -- Did San Francisco 49ers coach Jim Harbaugh make the right call in 2012 in going with Colin Kaepernick over Alex Smith at quarterback?

"You're going to have to ask coach Harbaugh that," Kaepernick said with a shrug. "I'm just trying to do my job."

OK, then does Kaepernick think he was the right choice?

"I'm not going to say that publicly because y'all are going to try and make it sound like something else," he said. "But, I do feel like I'm a good player, yes."

Fair enough. What about from Smith's perspective, did the Niners make the right choice in choosing Kaepernick over him?

Smith laughed nervously.

"I'm not even going to answer that, man," he said.

Truly, and especially, with the two facing off Sunday at Levi's Stadium for the first time in a regular-season game since the Niners traded Smith to the Kansas City Chiefs for draft picks that turned into defensive lineman Tank Carradine and running back Carlos Hyde, you wouldn't expect to get more out of either player. But the question had to be asked.

ESPN NFL scouting expert Matt Williamson, meanwhile, liked the move back then and likes it now … even if he's hesitant to call it an overwhelming success for the 49ers.

"They got something for Smith; they didn't just give him away," Williamson said. "Smith has played better than expected. I was very high on Kaepernick coming out of college. I still am. Not as high. He hasn't progressed as much as I thought he would."

Since the beginning of the 2012 season, the two have the same passer rating as starters -- 93.7. Smith is 19-8-1 as a starter while Kaepernick is 19-8. Kaepernick has thrown 37 touchdown passes and 15 interceptions, while Smith has 43 scores and 15 picks.

Based on those numbers alone, it would seem Smith has had more success, no?

Well, Smith did lead the 2011 49ers to the NFC title game. After Kaepernick took over for good in Week 10 the next season, Kaepernick led the Niners to the Super Bowl.

Last season, the Kaepernick-led Niners were in the NFC title game while Smith led the Chiefs to a first-round playoff exit.

And when you factor in everything they bring to the table, Kaepernick's total quarterback rating of 67.6 as a starter eclipses Smith's 54.5. And that's why Williamson would still choose Kaepernick over Smith.

"I think [Smith's] reached his ceiling," Williamson said. "He's better than Matt Schaub in his prime."

And Kaepernick?

"I still think he's a work in progress," Williamson said. "But even when he's not right, he's still dangerous. You can win a lot of games with him."

And yet…

"He hasn't progressed nearly as much as I thought he would," said Williamson, who mentioned Kaepernick's penchant for throwing every pass on a straight line.

"There's times when you have to be able to drop it in a bucket," he said.

Or else, you have to be a game-changer as a runner, which is Kaepernick's forte. Because in that same time span as starters, Kaepernick has nearly doubled Smith's rushing total, 1,126 yards to 666 yards, and has nine rushing touchdowns to Smith's one.

And also courtesy of ESPN Stats & Info, Kaepernick's average pass as a starter since 2012 has been 9.1 yards downfield, compared to Smith's 6.7 yard-average, the lowest in the league.

It's why Smith has been known derisively in his career as a "game manager." And why Harbaugh bristles at the notion.

"Not an accurate term," Harbaugh said. "He's a football player.

"I know Alex did the very best he could when he played here and he did great. We felt the exact same way. And when you do your best, you look back and you feel good about what you accomplished. That's the very nature of giving it your very best. Therefore, you can look back and feel good about the things that you accomplished. Very happy for his success. Not rooting for success for him this week, but always very happy for his success, almost all the time, for Alex Smith's success. This week not included."

Otherwise, there will be rumblings that the Niners should have stuck with Smith longer. Not that Williamson will subscribe to that theory.

"I think Kaepernick will be better than Smith ever will be," Williamson said.

All of which brings us back to the initial question, and to take Kaepernick's advice. What, then, would validate the Niners going with Kaepernick over Smith?

"Never been a big fan of comparisons," Harbaugh said. "Colin's play has spoken for itself."

Even if neither Kaepernick nor Smith would speak for themselves.