Not surprisingly the more casual fans on this board(don't mean that in a condescending way, just referring to those who aren't regular contributors in the weekly threads) are greatly overrating how good Alex Smith is...
He is not good at all, people. The reason why his numbers aren't horrible the past two years is because Harbaugh is one of the best coaches in the league, and he has changed the offense to deal with a "game manager." He has instructed Smith to take very few chances and to always err on the side of caution by taking a sack/throwing the ball away instead of taking any risk. This works decently when you have the defense and supporting offensive cast to carry your team. However, thats thing thing- SF has an awesome all around team. For example, most people probably don't realize that
PFF ranked SF the #1 o-line in all of football so far this year.
So yes, SF has been able to still be successful by having Smith take no chances whatsoever and letting the talent around him shine....but theres a real chance that Kapernick is a legit talent and can be a mid tier starting QB(lets say as good as someone like Joe Flacco for example) or better by playoff time if he gets more reps and continues to improve. And imo SF's supporting cast is so good that this improvement at the QB position would make them the best team in the league. Moreover, Kapernick showed enough in that one game that I think his downside is still around how good we already know Smith is(again, hes not that good...this media narrative about his improvement and his "protection of the football" is almost exclusively due to Harbaugh).
I don't think this is a particularly close decision. I think this is yet another case where many old-time coaches are afraid of "taking chances" in the same way that they are afraid to go for it when its mathematically correct on 4th down. I forget the name of the cognitive bias, but I've heard it discussed with regards to blackjack before- Even though some people know that its mathematically correct to hit on some cases(when you have 16 and dealer shows a 9 for example), people are inclined to take the passive route because if they take the aggressive(yet mathematically correct) route and don't succeed they feel as if they contributed to their failure moreso, whereas if they take the passive route and fail they can just blame the cards(or their players in the case of NFL decisions).
I also think that theres a clear trend of QB prospects developing much quicker than in the past. This is very clear to see with young QBs playing in year 1(and succeeding) much more than in the past. I don't think this is limited to football either- guys like Kyrie Irving and Anthony Davis are studs from day 1 in the NBA too. I think its the pre HS/HS/NCAA development process becoming more and more optimal for elite prospects to the point where they are now pro league-ready by the time they hit the pros. I think that NFL coaches have been too slow to adjust for this, and they hang on to prospects like Alex Smith and Mark Sanchez for far too long. I think that in today's NFL its optimal to decide quickly on whether or not these guys "have it" or not. Smith doesn't "have it", we already know this and its holding back a title contender to keep pretending that he might suddenly discover it.