The popular assertion that Kaepernick has been regressing for years now and that he's had consecutive bad years is one of the biggest myths thats really out of control. In the 2014 season, Kaepernick passed for 3,369 yards, 19 touchdowns, 10 interceptions, and a passer rating of 86.4. It's hard to fathom how anyone who follows NFL football can consider that a bad season. It's certainly not setting the world on fire, but those are efficient, above average numbers. If you do think that season is bad, then you should also believe that Flacco should not even be an NFL quarterback, because those numbers are similar to the numbers that Flacco records every year consistently.
In 2013, in his 10th year in the league, Eli Manning threw 18 touchdowns and 27 interceptions. That's a level of bad that many quarterbacks never rebound from. Kaepernick has never approached a level of play that poor. Also that year, Flacco threw more interceptions than touchdowns as well: recording 19 touchdowns and 22 interceptions. Go down the list of NFL quarterbacks, outside of the few truly elite signal callers, and you will generally find a season where they played well below their usual level of productivity. It happens.