With a defense that ranks near the top of every statistical category -- a defense that Jerry Rice told HuffPost was "unquestionably the best in the NFL" -- the choice for Harbaugh essentially comes down to risk. Smith will rarely hurt you but he will rarely win games either. Kaepernick, at least thus far, seems to be the home run hitter who is also willing to hit singles when needed. In other words, the best of both worlds.
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