We all know Alex isn't Peyton, Joe, or Drew.
I think he understands that, as well.
Can he get better? Absolutely. And SF is the best place for him to do that, and now that he's got some more weapons, and more familiarity of the offense (this goes for all of the players), I think we'll see improvements all around.
Alex will sign his contract, and will be back for the 49ers.
I also think that they will give Josh Johnson a look, at the very least, but I think if for whatever reason Alex doesn't return (doubtful IMO), they will look for a stop gap while Kaepernick is further groomed, and I think they have faith that he will be able to take this team over very soon.
I was bummed that Peyton chose the Broncos, but then again, I wondered how that move might affect our team chemistry, not to mention we don't know how well his neck will hold up. I highly doubt he was taking any blind side hits from 350lb men while he was throwing for prospective teams, so really his abilities after these surguries are still a big question mark.