Why Kyle Shanahan, 49ers moved on from Colin Kaepernick

Golic buys Shanahan's comments on Kaep's fit with 49ers (0:57)

Mike Golic understands what Kyle Shanahan is saying when he says Colin Kaepernick doesn't fit well in his offense. (0:57)

PHOENIX -- As the San Francisco 49ers honed in on filling an empty quarterback depth chart in the opening days of free agency, general manager John Lynch received information that made him believe Colin Kaepernick was close to signing with another team.

"At one point, there was some information as were kind of going through our own quarterback thing and it's kind of what happens in free agency," Lynch said. "You get information and you set the market for guys you're talking to and things and there was information that came to us and I know that thing has blown up and I don't want to get in other people's business but there was some information that he was very close. Obviously it didn't happen. I don't know what happened."

But Lynch and coach Kyle Shanahan do know what happened with Kaepernick in San Francisco. After meeting with Kaepernick before free agency, the 49ers have not had any contact with him and signed veterans Brian Hoyer and Matt Barkley, likely ending Kaepernick's time with the team after six seasons.

While Shanahan has proved flexible with his scheme based on the talent in place in previous stops as an offensive coordinator in Houston, Washington, Cleveland and Atlanta, this is Shanahan's first chance to build a roster in the mold of what he wants. That doesn't mean he won't adapt to some of the talent in place but he and Lynch have a set idea of what they're looking for at every position moving forward.

At quarterback, that happens to mean eschewing the zone-read based offense best suited for Kaepernick's skills in favor of the modernized West Coast offense Shanahan has used with more pocket-oriented passers.

"Colin's had a great career, and he's done some really good things," Shanahan said. "I think Colin has a certain skillset that you can put a specific offense to it that he can be very successful in. When we first looked at it, you've got to look at each quarterback and what type of offense you want to put in. That wasn't necessarily the direction I wanted to go. I wanted to put in a different type of offense."

In sorting through Shanahan's previous matches of scheme and quarterback, the best parallel had he decided to keep Kaepernick would have been to replicate the model he used with Robert Griffin III in Washington. That system worked for one season but was hard to sustain because of the added injury risk the running possibilities for Griffin created.

If the 49ers had opted to bring Kaepernick back, he would have had to come back closer to the 225-pound version of 2013 and the 49ers probably would have had to bring in more quarterbacks cut from a similar cloth. That style is harder to duplicate than the direction the 49ers chose to go.

So when Shanahan and Lynch evaluated free-agent quarterbacks, they sought players who are better suited to make quick, accurate decisions with the ball. That they found some familiarity in Hoyer made signing him quickly that much easier.

"All these questions people ask about what I like in a quarterback, Brian is like that," Shanahan said. "Brian is obsessed with the game. He will learn your offense, he will be able to execute and run it and that gives other guys a chance to perform in your offense. If your quarterback can't execute it and go through it, then it doesn't always matter what the O-line and receivers are doing. Brian is a very smart guy who works at it, will hang in the pocket and is fearless to keep his eyes down the field and move the ball to the right spots and it gives people a chance to be successful."

Although Shanahan has never worked with Barkley, he said he saw similar traits that make him believe he could be a suitable backup to Hoyer. Citing Barkley's history playing in big games as far back as college and his progress in a short stint as the Bears starter a year ago, Shanahan also believes there's still some upside for Barkley.

"He's battle tested in that way," Shanahan said. "He's gone through the pressure in college, the pressure of the draft, the pressure of being in the NFL, going through some different teams. Even watching him in Chicago this year, he played better this year than he has throughout his career."

Of course, Shanahan and Lynch are quick to acknowledge that they are far from done revamping their quarterback group. They still need a long-term answer at the position though they've made it clear they are willing to have some patience to make that happen. Even if that player doesn't arrive this offseason, the 49ers will need to add another quarterback or two at some point.

It's a safe bet one of those will come from the NFL draft, even if it's a mid-round prospect Shanahan can develop.

"We'll look to add anything we think that can really help us," Shanahan said. "I'm very happy with the two we've got. We're not only going to take two to camp so we've got to see how the draft works out and then you see what else is out there if it doesn't work out the way you want."

It's too early to predict the names of the next quarterbacks to land in San Francisco but given how the 49ers have approached the position this offseason, it's now much easier to determine the scheme fit Shanahan and Lynch seek.