San Francisco 49ers would be better off with Colin Kaepernick on roster

Colin Kaepernick remains unsigned, but that does not change the fact the San Francisco 49ers would be better off if he was still on the team.

The Seattle Seahawks may not have signed Colin Kaepernick, but in explaining their decision, Pete Carroll said what too many people have been unwilling to admit: the former San Francisco 49ers quarterback is a starter in this league (per NFL.com).

He is the second NFL head coach to state that opinion, following the Baltimore Ravens’ Jim Harbaugh. Meanwhile, Kaepernick’s continued unemployment and the Seahawks’ explanation that they did not want two starters on the roster have both raised eyebrows. But what did not provoke as much bemusement was the 49ers parting ways with Kaepernick. He opted out of his contract and the Niners made no attempt to re-sign him.

That decoupling was accepted as the right move for both parties. Yet, even though the 49ers have a quarterback that fits Kyle Shanahan’s system in Brian Hoyer, the decision not to make a run to keep Kaepernick deserves further scrutiny.

Though signing a quarterback familiar with Shanahan’s scheme in Hoyer makes sense, Kaepernick is comfortably superior to the 49ers’ current backup in Matt Barkley and played significantly better than San Francisco’s win total suggested in 2016.

In a recent piece stating discussing 15 backups who are superior to Kaepernick, the MMQB’s Andy Benoit criticized him for an unwillingness to throw from the pocket, a lack of touch and an inability to pass while on the move.

But, in a film room piece for 49ers Webzone, Rich Madrid cited multiple examples of Kaepernick successfully doing all three of those things on the field last season.

His play on the field translated into 16 passing touchdowns and just four interceptions. Those are impressive numbers and are easily superior to those of Barkley, who threw for eight scores and 14 interceptions in just seven games as he filled in for an injured Hoyer with the Bears.

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Kaepernick, per Football Outsiders, ranked at No. 23 in total QBR, seven spots above Barkley. However, Barkley was ranked above Kaepernick both in their Defense-adjusted Yards Above Replacement and their DVOA metric.

Hoyer outperformed both Kaepernick and Barkley in all of those metrics, but from an extremely small sample size having played just two games in 2016 before getting injured. He completed 67 percent of his passes, throwing six touchdowns while taking care of the football — not throwing a single pick, with his completion percentage comparing favorably to that of Kaepernick (59.2) and Barkley (59.7).

Yet, while Hoyer can be considered something of a safe pair of hands, he does not have the mobility nor the upside of Kaepernick and his limitations have previously been laid bare in the big-game spotlight, such as in the Texans’ dreadful 30-0 Wild Card Round loss to the Chiefs in January 2016.

Barkley, meanwhile, has shown himself to be an extremely mistake-prone quarterback who, like Hoyer, does not possess the mobility of Kaepernick.

There is an obvious advantage in having a quarterback like Hoyer to guide the team through a transition to a new offense and it is easy to understand why Shanahan would want to save time by not having to have a starter to learn the scheme as Kaepernick would.

However, there would have been no harm in having Kaepernick learn the system while competing with Hoyer. And in that sense it is somewhat perplexing that Shanahan and general manager John Lynch — who said the 49ers would have cut Kaepernick had he not opted out, per Pro Football Talk — did not want to keep him around.

Kaepernick would have been able to put pressure on Hoyer had he been kept around. With Hoyer starting ahead of Barkley and rookie C.J. Beathard, there will be a limit to how far this 49ers offense can go, at least in the short term.

Next: NFL 2017: Predicting All-Pro offense after OTAs

And when those limitations will become apparent, fans may question why, after he performed well on a terrible team, the Niners did not even consider keeping hold of Kaepernick.