I believe the first thing is that the offense was predicated around him this year. In years past, Gore was the 1st option as they would pound first then allow Kaepernick to improvise on the roll out or out of the pocket. He hasn't learn how to read defenses yet. You look at Brady--many people marvel at his eyes as he does not stall on a read and looks through his progressions with pinpoint accuracy. Kaepernick, as mentioned by Seahawks and other teams' defenders--has been unable to go through his progression. I think its too much to expect him to be in the pocket and only run when need be. I don't know if you're ever going to fix him. It'll have to be under a new O coordinator and probably a new offensive philosophy.