One reason I think Kaepernick's passing acumen is a bit slow to develop is that the niners are seldom trailing in games and Harbaugh is generally a pretty conservative coach with the lead. Just not enough reps in hurry up mode or ever really "needing" a score.
Sometimes QB skills develop out of sheer reps and necessity. Some QBs are always trying to milk every second out of the play clock or playing catchup due to a poor defense and IMO some of their effectiveness comes with the experience of being in those situations a lot.
You could argue chicken or the egg here, but I think Harbaugh needs to loosen the reigns on Kaepernick for the sake of his development as a passer. Nobody ever became an elite QB by being a game manager (and no Flacco isn't an elite QB)
ETA: Considering how seldom Kaep has to try to win games by coming from behind, he actually does a pretty good job of it. This is probably the reason why I think the best is yet to come with him.
One has to figure why expectations are already so high for him. Is it because he plays on a team that's a contender due to having a good defense and consistent coaching? Alex Smith didn't have those expectations with that in 2011. Is it because of his physical attributes? Sure, but that doesn't make him a good QB alone. Is it because he is in a good passing offense? That's a flat no, because the passing offense was weak in 2011 again with Smith as starter.
Expectations are high of him because
1) Lots of publicity (both good and bad type) and hype
2) He's on a good team with all the other key parts to win a championship
3) He replaced a good QB after a QB controversy where it wasn't clear who the best option was
I'm not saying Alex Smith was/is a better QB for the 49ers than Kaep, but I do think he's a better passer right now and that they would still be a perennial NFC championship game contender.
Publicity goes with any athlete who some (see: Ron Jaworski)
expect can change the position , like Russell Wilson has as well, who is also on a good team with a great defense. I don't fault an athlete who earns endorsement deals either. That's up to a particular brand investing in a commodity. Kaep's jersey is a big seller, so brands naturally would want to attach Kaep to their products.
Cam Newton and Andrew Luck have high expectations as well, but right now people here are questioning Kaep more than both of them. That's fair enough because of Kaep as a pocket passer, yet Luck threw more INT's in this post season than Kaep did and in fairness to Kaep, he helped take his team further into the post season than both aforementioned QB's. Those who question Kaep for post season INTs should equally question Luck for his. That would make this, well, fair.
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In 2011, David Akers was the leading scorer for the 49ers. Smith had a bunch of donut hole games as far as passing TDs that season. This season with KC, he also had a bunch of donut hole passing TD games. Yet he has Charles as his RB, where he can dump off to for multiple TDs that hardly travel through the air (see: the game against OAK where the ball traveled only 13 yards in the air for multiple scores where Charles did all the rest of the work).
Smith has been in the NFL since 2005, Kaep since 2011. So far the 49ers with Kaep has had Crabs and Davis post better numbers than with Smith. Boldin this season has had one of his best seasons since his days in AZ. Davis posted his best season since 2009 with 13 TDS (which matched this season), but he also caught 3 TDs from Shaun Hill, and a lot of his production came from the 49ers being behind in games.
A key stat which I had posted in the 49er team thread was where the offense was on 3rd down over the past three regular seasons. They have been traditionally poor in that stat over the past decade with Smith. So far, they have improved that quite a bit with Kaep under center. It could be a combination of his legs and the threat of the run with Kaep, but that's a tangible improvement either way.
All this adds up to Kaep being the right choice at QB over Smith.