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If you read Alex Smith's scouting profile from before the 2005 NFL draft, his biggest weakness was that he didn't throw deep passes as a quarterback in college. Not much has changed since then, as Smith will regularly check-down to a running back or look for the nearest tight end.
On the rare occasion that Smith does throw the long ball, it often flutters in the air, losing its trajectory. When the ball does retain its spiral, it's regularly overthrown or under-thrown in relation to the target. In either case, Smith's ball is difficult to catch.
This normally isn't noticeable on first or second downs, which are usually running plays or short-range check-downs, but in 3rd-and-long situations, the deficiency with the deep pass is particularly glaring. Last year, the 49ers finished 23rd in the league on third-down conversions, and this year, they aren't doing much better.
However, that could improve with Colin Kaepernick, as he's shown in two starts that he can make intermediate throws down-field with high accuracy and velocity. The ability to extend drives and score touchdowns is crucial, especially now that the 49ers revealed that their kicker, David Akers, has been struggling with a pelvis injury, which may explain his sub-par performance this year.