The Alex side of the story
The only reason he didn't start was because he was injured. He never lost his job and never got benched. The 49ers were planning on starting him all week against the Bears and were then surprised that he didn't clear the concussion protocol. When he wasn't cleared at the beginning of the week against the Saints the coaching staff decided to go with Kap because then there is no guessing who is going to start, and there was a chance that Alex wouldn't be available again. He didn't get cleared until Friday. Plus, the game against the Bears went well enough that they weren't worried about Kap in the Saints game.
In the last 5.5 quarters that Alex played in he was 25/27 for about 300 yards, 4 TD's, and 0 Ints. That is an amazing level of play.
He is running this offense at a very efficient level right now.
The Kap side of the story
Kap did amazing considering that these were his first 2 starts. I can certainly see him as the future. And if the 49ers name him the started right now I will not be saddened or worried about the fate of the team. However, he has not played at the over the top level that some people give him credit for. He has some amazing skills: arm strength, speed, size, ability to throw deep, throw into tight windows, and avoid the pass rush. Having said all of that I don't think that he is ready yet. Frank Gore is helping with some of the pre snap reads. That does not scream guy who is totally ready to me. He has made some bad decisions (the pick being 1 of them).
The 49ers are about to have at least 3 new players in the lineup on a regular basis who haven't had a lot of playing time yet. Brandon Jacobs, LMJ, and AJJ. These guys are going to be filling in for KH and KW. It is one thing to mix Kap into the lineup with a bunch of other players who already know the system like the back of their hand. They can help fill in the gaps for Kap (like Gore helping on pre snap reads). Trying to mix in BJ, LMJ, and AJJ all while trying to get Kap fully acclimated would be a recipe for disaster in my opinion. With Alex as the starter he can help guide those guys. Kap not only can't totally help guide those guys he still needs a little guiding himself.
The Jim Harbaugh side
During the 2 games that Kap started he wouldn't announce who the starting QB was early in the week because he wanted to give his young QB any advantage that he could. Including the other team knowing that they only have to prepare for Kap. This week he will announce it early because it will be Alex. And teams have already been preparing for Alex and he has had success so it wont be a detriment to his success. Alex Smith is a captain of the team. I think that carries some weight (it may not but I think Alex is much more respected in the locker room than he is here on NN). Harbs called him the starting QB in Monday's press conference. I know he didn't name him the starter and I know he didn't say that Kap is the backup. But I think that is his way. He never calls the backups backups. He never calls the inactive guys the inactive guys he calls them developmental players.
So, I am going on record as saying that he will name Alex. I have no secret information. I am just some jerk on a couch. But I wanted to put it on record what I thought would happen before it happened so I can look like a genius when I am right. Then I will tell everybody how smart I am and how well I know the team. When I am wrong...??? I will just delete this post and deny it ever happened. So if you are reading this then that must mean I was right. Feel free to post praise in the comments below.
Kap or Smith it doesn't really matter to me. Go 49ers!