If you watched the 49ers all season and saw the difference between Smith and Kaepernick, you'd know how wrong your statement is. Kaep didn't just benefit from an excellent team. He greatly increased the capability of the offense, and that's speaking purely from a pocket passer standpoint.
Kaepernick's accuracy is tremendous. To use a baseball analogy, Smith could throw strikes but Kaepernick can paint the corners.
In addition, Kaep knows how to move in the pocket to avoid pressure without resorting to scrambling. So many cases where Smith would've taken a sack or thrown the ball away, but Kaep slides a little, buys time, and completes the pass.
Kaep did not show consistent ability to correctly recognize defenses and would sometimes freeze with indecision, unable to properly read the D, go through his progression, and make a quick decision where to put the ball. That's where he needs the most work, which is pretty much like every QB with less than a full year's starting experience ever.
I'm not speaking about any other QB, just pointing out that dismissing Kaepernick's throwing ability is a mistake. Despite being a 49er fan, Luck is my favorite young QB. I am delighted there is so much young QB talent in Kaepernick, Wilson, RG3, and Luck to watch and enjoy.