I completely disagree with everything that you just said. This isn't a case of betting on upside. Kaepernick has already proven that he's good. He's been to back-to-back NFC championship games and a Super Bowl, has never had lower than a 2:1 touchdown to interception ratio, and has the ability to dominate with both his arm and his legs.
What evidence do you have to support your insinuation that Kaepernick isn't cerebral or is incapable of mastering the mental part of the game? He's been great ever since he took over as the starter in San Fran and he's paired with arguably the premiere quarterback coach in the league.
Knocking Kaepernick because of his supporting cast isn't fair, either. Should we question Peyton Manning because he's had Marvin Harrison, Reggie Wayne, and Dallas Clark to throw to (or now Demaryius Thomas, Eric Decker, Wes Welker, and Julius Thomas) or Tom Brady because he's gotten to throw to Randy Moss and Rob Gronkowski?
Holding the fact that Kaepernick has the ability to make plays with his legs against him is completely asinine. Aaron Rodgers (whom you mentioned), Cam Newton, Andrew Luck, and Russell Wilson all have the ability to make plays with their legs and are also great throwers. This makes them more dynamic, not worse quarterbacks.
