A certain CJ user named after a food item has gone on record saying that not only is Kaepernick a better QB than Dalton, but the person who chose to draft Dalton instead of Kaepernick should be fired on the spot.
Obviously, we can't directly compare stats because Kaepernick hasn't been the starter for an entire season yet (in fact he has only even played in one season's worth of regular season games in his career thus far.
But, you can take his averages and extend them across the year as though he were the starter all season. It won't accurately reflect what would have happened, but it should give a good idea how he would have performed.
Andy Dalton's stats for the 2012 season:
Passing: 329 completions on 528 attempts (62.3%) for 3,669 yards and 27 TDs to 16 interceptions.
Rushing: 47 attempts for 120 yards (2.8 YPC) and 4 TDs.
31 TDs total versus 16 interceptions and 4 fumbles (none as a runner, all came as the result of QB hits)
Kaepernick's stats for the 2012 season:
Passing: 131 completions on 209 attempts (60.1%) for 1,725 yards and 10 TDs to 3 interceptions (That is only counting the games he started or played a significant amount, 8 in total)
Rushing: 50 attempts for 304 yards (6.1 YPC) and 3 TDs (again, that is JUST the games he started or played a significant portion of)
13 TDs total versus 3 interceptions and 9 fumbles (7 of his fumbles were as a runner, only 2 as the result of a QB hit)
Now, lets extend Kaepernick's stats across the rest of the season as though he had been the starter all year.
Passing: 262 completions on 418 attempts (60.1%) for 3,450 yards and 20 TDs to 6 interceptions.
Rushing: 100 attempts for 608 yards (6.1 YPC) and 6 TDs.
Now to extrapolate the number of fumbles if he had started all year: 18 fumbles, with 14 of them coming as a runner and 4 as a result of a QB hit.
Total potential turnovers for both players:
Total touchdowns for both:
Now, again, my extended stats for Kaepernick don't indicate what would really have happened, but they give a decent idea of what his performance may have been like if he had been the starter all year.
My take on all this:
Kaepernick is quicker to run than Dalton is, but he also has ball security issues when he does. He fumbled 7 times last season as a runner, while Dalton did not fumble at all during a scramble. Dalton also had only 4 fumbles all year.
Dalton throws more interceptions, but he also throws more passes in general. He also had only 2 games last season in which he did not throw a TD pass, and 7 in which he threw 2 or more. In contrast, Kaepernick had 3 games in which he did not throw a TD pass and only 3 where he threw 2 or more.
Colin Kaepernick is a decent QB, but the only reason he went to the Super Bowl last year is because he was drafted by the 49ers. If the Jaguars had drafted him instead of Blaine Gabbert, he would have been watching the Super Bowl from his couch just like 29 other QBs. He is not good enough to make a bad team great single-handedly. He went to the Super Bowl because he got drafted by a team that was already very good without him.
In contrast, Dalton was drafted as part of a rebuilding project, and has been an important piece of his team's improvement.
So, if the draft were to happen over again, with the knowledge we have now, I'd still draft Dalton over Kaepernick.