Harkins: Kelly convinces 49ers that Kaepernick worth a big gamble

The San Francisco 49ers are taking a gamble that the 2012 version of Colin Kaepernick is out there somewhere.

The announcement came from general manager Trent Baalke at the Scouting Combine on Wednesday morning: Kaepernick will be staying with the 49ers.

Trent Baalke: Expects Colin Kaepernick to be with #49ers on April 1 when he's due $11.9 million.

— Eric Branch (@Eric_Branch) February 24, 2016

The move is surprising, given the steady decline of Kaepernick since bursting onto the scene in 2012, when he replaced Alex Smith mid-season and dazzled the league with his combination of strong arm and quick feet, helping lead the 49ers to the Super Bowl. It’s also surprising given that Kaepernick had three surgeries last season, will cost nearly $16 million against the salary cap and is no surefire bet to beat out Blaine Gabbert for the starting quarterback position. That’s not the kind of money you want to pay your backup, especially if that backup is playing second fiddle to a guy like Gabbert.

Kaepernick will be guaranteed $11.9 million if he is still on the 49ers’ roster on April 1 and the team would have saved about $8 million off that $16 million cap hit by cutting him.

New coach Chip Kelly has revealed very little about his plans for the quarterback position, at times seeming to go out of his way to praise Gabbert, while being non-committal about Kaepernick. That must have been subterfuge by design, because Kelly had to have turned around and convinced Baalke and the 49ers management that he could work with and develop Kaepernick.

Perhaps Kelly thinks he can do with the multi-skilled Kaepernick in San Francisco what he did with a similarly skilled Marcus Mariota at Oregon.

That seems unlikely to happen. Yes, Kaepernick has a strong arm. Yes, he can run. But can he read defenses properly? Can he adjust to wrinkles defensive coordinators will throw at him mid-stream?

These are legitimate questions. There has been chatter recently that Kaepernick is lacking as a student in the meeting rooms. Former 49ers receiver Michael Crabtree said as much, positing that Kaepernick needs to “get in those books and watch that film and know what he’s doing out there.” Those statements have been backed by others, including Steve Young.

Another concern is the question of accuracy. It has frankly never been a strength of Kaepernick’s, who has a 59.9 completion percentage in the NFL, which is actually slightly better than his 58.2 percent mark from college at Nevada. By comparison, Mariota completed 66.8 percent of his passes at Oregon, 62.2 percent as a rookie with the Titans.

Kelly must think he can help Kaepernick develop in ways Jim Harbaugh and Jim Tomsula couldn’t. He must also not be very sold on Gabbert, a journeyman who played decently for the 49ers last season but who has a career passer rating of 71.9 and has thrown nearly as many interceptions (31) as touchdowns (33).

Either way, in reading his own roster, the quality of the free agents out there and the odds of getting a quarterback he likes at the No. 7 spot in the draft, it appears that Kelly decided Kaepernick was his best option.

Whether or not the Kelly-Kaepernick duo will shine remains to be seen, but Kelly has convinced the 49ers brass to take a multi-million-dollar gamble that it will.

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