(with a different QB thing)This is addressing likely other options.
Especially regarding the first of 2 years. I don't think SF would have came close as they have with another QB (If Jets had a Kaepernick they would have won like 4 Super Bowls). His yards per attempt was 8.32 and one of the best in the league at throws 15 yards or higher which made them into not only the favorite to go to the Super Bowl but win it. W/ Smith they were simply contenders. In the playoffs in the Green Bay game they couldn't defend his run or pass, making the wrong guesses as to what to defend. Atlanta - they fell behind early but Kaep w/ his 5 incompletions and 11+ YPA they rallied and were able to win. Against Baltimore, they fell behind fast and early. Usually that causes QBs to play worse, taking more risks incurring bigger losses. Pass interference and defensive holding could have been called on the final drive according to the rulebook. I just didn't understand calling multiple rollouts since it condenses the defenses, limits to eligible right side receivers, and cuts the field in half(generally - SMU completed a crazy tip-toe catch on the left side of the back end zone off of a right side rollout in one of the top highlights of the college football season 2 years ago to tie the game to send it to OT in a game they eventually lost).
Second season - Seattle has Kaepernick's number. They intercept him more than all the other scheduled teams do combined. However, rather than play it safe Alex Smith Kaepernick rifled a high pass to Boldin to take the lead but could have been picked off it was thrown lower or w/ more loft. Teams need QBs not afraid to make those throws to threaten Seattle. They would have ate up Alex Smith or possible available free agents and draft options at the position. Kaepernick completed key 4th & 3rd down on the drives, I think the no huddle(they absolutely had to - Vick forced nearly an identical throw off a no huddle in their playoff game against Green Bay) forced them to hurry up and make a decision rather than taking time to figure out the best play to call in that situation.
On edit - we also don't have the benefit of seeing what the play looked like right before the ball was thrown though I suppose you could sign up and pay to watch full NFL games at NFL.com and watch the 11on11(aka game film) camera settings.
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