The problem with Kaepernick is, despite his obvious physical talents, he seems to lack the ability to properly read defenses and adjust coming out of the huddle. He tends to lock onto one play and one play only, and it has cost the Niners repeatedly. Frankly, with some adjustment, I think Kap would be effective as a tight end.
I also agree with the other posts... the FO should NEVER have treated Harbaugh in that manner. Jed York and the rest of them seem determined to shitcan that team back to the bad old days of the late 1970s.
Unless he runs the ball himself and that isn't working as well for him.