Going from second to third on the depth chart would look like a regression for Kaepernick, but it might not mean much for the long term. Circumstances have changed. Alex Smith outperformed expectations last season, earning a new contract and tightening his grip on the starting position. The team signed Josh Johnson, Harbaugh's former quarterback at the University of San Diego. Scott Tolzien, another passer the 49ers liked coming out of college, has gained some seasoning.
Kaepernick was facing a significant transition from the system he ran in college. His development was going to take time. It'll be good for him to get extensive reps in the preseason, but Johnson will need playing time, too. The goal, of course, is to upgrade the quarterback position, not make sure Kaepernick appears instantly worthy of the second-round choice San Francisco used to select him. As coach Jim Harbaugh said on the day the 49ers drafted Kaepernick: "We believe in competition. We believe in earning positions around here."
The 49ers ideally would have found competition for Kaepernick last offseason. A lockout-shortened signing period complicated those efforts. That cleared the way for Kaepernick to land the No. 2 job unopposed. The 49ers got away with having an inexperienced backup when Smith started all 16 games, plus two playoff games, without encountering the injury problems that sidelined him in past seasons.
There's no precedent for developing quarterbacks drafted in second rounds. Each situation has its own dynamics. A year ago, developing Kaepernick on a fast schedule seemed important. Those still skeptical of Smith might feel that way yet. But Johnson, with more experience than Kaepernick, might be better prepared to take over a playoff-caliber team on short notice, should Smith struggle or suffer an injury. It's up to Kaepernick to prove otherwise.
As the chart shows, five of the nine second-round quarterbacks drafted from 2007 to 2011 were third-stringers or had been released heading into their second regular seasons. Chad Henne and Kevin Kolb were second string. Andy Dalton remains a starter heading into his second year. Brock Osweiler, a second-rounder in Denver this year, hasn't had a second season, obviously.