Big deal? Not really.
Kaepernick, the 36th overall choice in his draft class, is one of five quarterbacks since 2001 drafted between the 30th and 39th picks. Three of the four others spent at least some of their rookie seasons higher than third on their teams' depth charts.
A quick review:
2007 Philadelphia Eagles: Kevin Kolb, chosen 36th overall, entered the regular season second on the depth chart behind Donovan McNabb after veteran backup A.J. Feeley suffered a broken hand in the final game of preseason. Feeley returned to the No. 2 role, but Kolb overtook him late in the season.
2002 Washington Redskins: Patrick Ramsey, chosen 32nd overall, opened the regular season third on the depth chart behind Shane Matthews and Danny Wuerffel. Ramsey missed 16 days of training camp during a contract dispute, setting back his efforts to beat out Mathews and Wuerffel, who had played for then-Redskins coach Steve Spurrier at Florida. Ramsey wound up starting later in his rookie season.
Every situation is different. Kaepernick did not put up impressive numbers during the preseason. Starter Alex Smith has not been durable or consistently productive to this point in his career. It's fair to question whether the 49ers should have done more to bolster the position, but there is precedent for slotting a player drafted as early as Kaepernick in the No. 2 role.