Alex Smith is a good quarterback, and there are plenty of stats and quotes to back that up. In tight end Vernon Davis' opinion, Smith is still their guy, and in coach Jim Harbaugh's opinion, Smith plays at a very high level.
However, there are five critical weaknesses to Smith's game that ultimately cost him the starting job, so let's review:
Alex Smith was sacked 44 times last year, more than any NFL quarterback in the league, and he was on pace to hit a similarly dismal total this year. It's not because Smith plays behind a terrible offensive line. On the contrary, the 49ers recently won their second Madden Most Valuable Protectors award by Hall of Fame coach John Madden.
So why is Smith sacked so often? It's by design. Because Smith lacks mobility in the pocket and struggles to find open receivers down-field, his history of throwing costly interceptions in traffic has been mitigated by taking designed sacks. If Smith can't find an open man down-field and cannot escape pressure in the pocket, he eats the sack. The problem with too many sacks, though, is that a team losses scoring opportunities and puts more pressure on its defense to win a game.
Conversely, Colin Kaepernick has excelled at escaping pressure in the pocket and extending plays to create scoring opportunities.
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.
Remember former 49ers quarterback Steve Young? He could beat defenses with his arm and his legs. He was a dual-threat that drove defenses insane. If they played too deep on coverage, Young would take off on the run, but if they blitzed Young at the snap, he'd find an open receiver immediately.
Unfortunately, Smith doesn't present the same type of duel threat that Kaepernick does. Kaepernick is averaging 6.4 yards per carry on the ground, while Smith has averaged 3.6 yards per carry throughout his career. Kaepernick also has four rushing touchdowns this year, and he's only started two games.
When you look at top quarterbacks around the league, it's important that a quarterback have mobility in the pocket (e.g. Drew Brees) or be able to extend plays on the run (e.g. Robert Griffin III). The worst-case scenario is having a quarterback that can't dodge pressure or beat defenses with his legs. With Kaepernick's mobility, the 49ers can extend plays through improvisation.
Last year, Alex Smith had six game-winning drives, but this year, Smith has struggled to rally the team from deficits. In their two losses to the Giants and Vikings, the 49ers failed to get the passing game going. However, when Smith left the Rams game with a concussion, the 49ers were losing, but Kaepernick helped rally the team to a tie. Comeback ability is a must in the NFL, especially when the playoffs come around.
Smith has only played two full seasons in his eight-year career, primarily due to shoulder injuries that damaged his throwing mechanics. Factor in concussions and the volume of sacks that Smith takes, there ought to be concern about Smith's durability and reliability. With Kaepernick's mobility and ability to extend plays, devastating hits to the quarterback position don't appear to be an issue.
It's not that Smith is a bad quarterback. On the contrary, he's improved immensely under coach Jim Harbaugh. In the absence of Colin Kaepernick, Smith would be the de facto starting quarterback, but the mobility, athleticism and big-play ability that Kaepernick offers is too valuable to ignore, and that's why Harbaugh is making the switch.