Totally agree on your assessment of Kaepernick as a football player. What people lose sight of is that in his first two seasons, CK had the benefit of both a Top 5 Defense and game plans drawn up by one of the best coaches of this era, Jim Harbaugh.
And even Harbaugh was only able to take CK so far — CK’s regression started in Harbaugh’s last season, once there was a large enough bank of film to study his tendencies.
Truth is that the only hope a team has of being successful with CK is to structure their entire offense around him (and even then it’s a slim hope). His abilities to read defenses or play from the pocket or control time of possession are all below average.