I touched on this in the opening slide and I'll elaborate here: Alex Smith and Matt Cassel are very similar players. Both are game managers, both have struggled when placed outside their comfort zone and both benefited from being in the right system.
Before Jim Harbaugh came to San Francisco, Alex Smith was a bust. Plain and simple. There's no arguing that Smith was a decent quarterback, as he was downright awful in his early years. His rookie year he threw one touchdown and 11 interceptions, good for a quarterback rating of 40.8. Woof.
Smith certainly improved over the years, even before Harbaugh became the head coach, but he didn't excel until Harbaugh took the reins. In the five years before Jim Harbaugh became coach of the 49ers, Alex Smith threw 51 touchdowns and 53 interceptions. In the two years under Harbaugh he had 30 touchdowns and 10 interceptions.
Was it a matter of simply putting everything together? Possibly, but the more likely explanation is Harbaugh's offensive strategy of pounding the ball and not relying on Smith to win games. With defenses stuffing the box to stop the 49ers' atypical run formations, Smith had open lanes that weren't there under Mike Nolan and Mike Singletary.
Cassel was in a similar situation before the Chiefs dipped into their pockets for him. When Tom Brady went down in the first week of the 2008 season, to these same Chiefs, the Patriots were written off as non-contenders. Insert Matt Cassel and the Patriots became an 11-win team, barely missing the playoffs. (How does 11 wins not get you into the playoffs, by the way?)
Cassel was sensational in 2008, throwing for 3,693 yards, 21 touchdowns and 11 interceptions. Much like how Smith benefited from Harbaugh, Cassel was the wonderboy of Bill Belichick. Yes, Cassel had an incredible year in 2010, with 27 touchdowns and 7 interceptions, but look at his other three years in Kansas City and that one is clearly the outlier.
Smith was a product of the system in San Francisco. The Chiefs made the same mistake with Cassel four years ago, yet they still haven't learned. Smith has shown he can guide his team deep into the playoffs, but without a strong foundation around him he is just another average quarterback.