There has been a lot of things that Kaepernick did well in his earlier days, but he has definitely gone backwards this season and last. It hasn't all been down to him, the o-line has gotten progressively worse, and there has been some downright criminal play calling at times. The underuse of Vernon Davis last season was truly baffling, while his refusal to run with the ball this season hasn't helped either, there have been many times that he has had space to move into but has turned down the chance. The flip side is that he has made some errors that even rookies would get stick for, like the play in the link where he fails to read that the Rams have over committed to the run, and that as a result Torrey Smith is wide open and would have one safety to beat to score a TD.
http://www.nfl.com/videos/nfl-game-highlights/0ap3000000570028/49ers-Colin-Kaepernick-doesn-t-see-open-receiver