To quote coach Mike Singletary, it's because Smith "gives us the best chance to win at this particular time," as he said on his radio show Tuesday. Of course, that's been a familiar refrain regarding every decision he's made this season.
But Alex Smith is 1-6 as a starter this season and 17-30 in his 49ers career; Troy Smith, who took over in October after Alex Smith was injured, is 3-2. So whether Alex gives the 49ers a better chance to win is very debatable.
The general feeling is that the Niners can open up their playbook a bit more with Alex Smith on the field. He's been with the team since the start of training camp, knows the protections and feels more comfortable executing the offense. Troy Smith had to work with a limited playbook because he was signed at the end of training camp, and although he's capable of making big plays, he frequently attempted risky throws into double coverage.
The change is odd for another reason. The 49ers play the Seattle Seahawks this weekend with their season hanging tenuously in the balance. If they lose, their hopes of advancing to the playoffs come crashing down. Is this the time to start a quarterback who hasn't played in six weeks?
While Troy Smith is certainly more dangerous outside the pocket, he has also slumped of late, failing to complete half his passes the past two games. He has also been sacked 16 times in his five starts (by comparison, Alex Smith has been sacked 13 times in six starts), an indication he holds on to the ball too long. In last Sunday's 34-16 loss to the Green Bay Packers, Troy took a sack on a second-down play from the Green Bay 2-yard line when he should have thrown away the ball. Instead of a touchdown, the Niners had to kick a field goal.
By his own admission, Troy Smith has said his "decision making" needs to improve. His coaches agree with that assessment.
In the end, this could well be an audition for Alex Smith, who has four games left (assuming Singletary doesn't switch back to Troy Smith, an option he left open) to show teams he has ability to start somewhere next season. He's in the final year of his rookie contract and won't be back.
That makes him a desperate quarterback. And since these are desperate times for Singletary and the 49ers, it might turn out to be a good decision.