San Francisco 49ers: Which Quarterback Should Start for Chip Kelly in 2016?

2. Colin Kaepernick

It’s true that Gabbert outplayed Kaepernick last season, but there’s a reason I said Kaepernick would still go significantly before Gabbert if you were to re-draft the 2011 season with today’s knowledge. His highs have been higher than any quarterback from his class other than Newton.

With Jim Harbaugh, Kaepernick soared. He not only made the Super Bowl as the starter in 2012, but followed it up with the best quarterback season by a 49er since Jeff Garcia in the early 2000s.  Remember, he threw 21 touchdowns to eight interceptions, throwing for 3,197 yards and adding 524 more on the ground. He was a true duel-threat quarterback, able to destroy opposing defenses with both his arm and legs. No, his accuracy wasn’t as high as it could have been, and in retrospect, you can see some flaws in his game he’s never patched up, but it was a legitimately great season that entirely justified the contract extension he signed before the 2014 season.

His 2014 season was certainly a down year, and 2015 was an injury-plagued disaster, but we’re not talking about ancient history here—it was only two years ago that Kaepernick was regularly being discussed as one of the best quarterbacks in the game. No one else who could start for the 49ers in 2016 has had a year nearly as good as Kaepernick has had.

There’s reason to hope that, with a new offense that seems tailor-made to his particular skill set, Kaepernick could re-discover that form that made him worth his contract extension. If the 49ers were tight against the salary cap, Kaepernick’s deal would make him a logical cap casualty, but with room to spare, why not give him one more chance with Kelly to see if he can be the guy you thought he was once upon a time?

Next: A Fresh Start