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The Case for
Just watch the Monday Night Football game against the Chicago Bears. He looked phenomenal. The Bears have one of the best defenses in the league. Kaepernick went 16-23 for 243 yards and two touchdowns. He can run, he can throw, and he also proved he can make the reads that are necessary to be a starting quarterback in the NFL.
He has the physical tools that Smith lacks. Alex Smith has good physical abilities. He can run, he has a good arm, but he is no Kaepernick. Kaepernick's running ability is better. His arm is a rocket! He almost took off Moss' finger with one of his throws. He has shown that he has the talent to become a great player.
Colin Kaepernick is the future, why not start now? The 49ers traded up in last year's draft to take the former University of Nevada star. He looks like the long-term option for San Francisco. He has had time to sit and learn. He has a good team around him. His growth will be much more rapid if he is given the reigns to this team now.
The Case against
He has only started one game! Let's not get carried away just yet. Backup quarterbacks often come in and have at least one good start. Matt Flynn, Kevin Kolb and others, have come into a good situation and looked great. Flynn is sitting behind a rookie in Seattle and Kolb hasn't looked like a starter in Arizona.
Defenses get better when they know what they are preparing for. Chicago had no idea what was coming when it took the field against Kaepernick and the 49ers. Kaepernick looked great, but let's not call him the second coming of Montana just yet.
He has no playoff experience. The 49ers want to improve on last season's success. That means they want to go to the Super Bowl.
Alex Smith has playoff experience. He won a playoff game against the Saints. Kaepernick barely has NFL experience. Even if he starts every game from here on out, he would still enter the playoffs without a full season of playing experience.
Winning in the playoffs requires a different personality. Kaepernick might have it, but he might not. The 49ers have seen what Smith can do. He can be good enough to get his team to the big game. They don't know if Kaepernick can do the same.