Ailene Voisin

Rookie Shanahan-Lynch era begins with Kaepernick question

Jim Tomsula, Chip Kelly, Kyle Shanahan. What do these three men have in common? Besides past or present head-coaching positions with the 49ers? Or the fact they were pummeled with questions about their coaching chops during their introductory news conferences at Levi’s Stadium?

Colin Kaepernick. The not-so-little matter of what to do with the mysteriously diminished quarterback.

That is the most pressing issue and the first order of business for Shanahan and general manager John Lynch, who sat alongside 49ers CEO Jed York on Thursday afternoon in what has become something of an annual affair. New coach, new coach, new coach. Three consecutive years of new coaches. Complicating the situation this time – or perhaps not, depending upon whether the task of reviving the 49ers becomes a truly collaborative affair – is that with former GM Trent Baalke exiled, York has entrusted his franchise (and the answer to the Kaepernick question) to a couple of rookies.

So, OK, Shanahan and Lynch are intelligent, articulate, poised and regarded within the industry as class acts. Presumably they will maintain their cordial relationship, divide their duties without a hiccup, with the GM controlling the 90-man roster and the coach having final say over the 53-man roster, and bring peace and collegiality to a franchise more familiar recently with back-room sniping, internal discord and a talent drain.

The hiring of Lynch remains the biggest head scratcher of the two moves. The distance between an NFL broadcast booth and a draft room is the equivalent of a cross-country trip. The drive can be treacherous. York is gambling that the skill set between microphones and talent scouting somehow translates, that Lynch displays a keen eye for personnel, a grasp of analytics and a feel for the nuances that separate, say, the resurgent Raiders from what’s left of a once-storied 49ers franchise.

Shanahan, who recommended Lynch in yet another coach-before-GM hiring scenario, was riding a Mavericks-size wave until his Atlanta Falcons drowned in last Sunday’s epic Super Bowl collapse against the New England Patriots. As the architect of the Falcons’ offense and Matt Ryan’s MVP regular season, the former offensive coordinator landed in the Bay Area more wounded bird than soaring eagle.

Asked for the zillionth time Thursday to explain why he called for risky passes instead of clock-eating runs late in the game, leaving him open to second guessing by everyone outside of New England, Shanahan adhered to the party line: “I called plays in that game the way I called them the entire year,” he said in thoughtful, measured tones. “That doesn’t mean I’m always right. That doesn’t mean it’s always going to work. It’s going to be hard living with that loss. Every play that didn’t work, I regret. But I can deal with it. It’s human nature when you get in the big moments like that to lock up, to hesitate, to try and take the easy way out. That’s something I wasn’t going to do or our team wasn’t going to do.”

His philosophy is to remain innovative and unconventional – avoid the group-think approach at all costs, apparently – which sort of explains his surprising and interesting thoughts about Kaepernick. The divorce isn’t final, yet.

“Colin, like any player, is someone I’m going to be watching a lot of tape on the next few weeks,” said Shanahan. “Before we can look at anything, you have to know who the players on your team are.”

Kaepernick, who is coming off two dismal and injury-hampered seasons and is set to earn $14.5 million unless he opts out of the final year of his deal, already has met with Lynch and expects to sit down with Shanahan soon.

That would be a meeting that, in the previous three coaching regimes, would have sprung leaks all over the building, with the involved parties spraying in different directions. Does Shanahan really believe he could rekindle a 49ers romance with a player who was molded by Jim Harbaugh and became virtually unrecognizable under Tomsula and Kelly? Who was never the same after throwing the errant pass into the end zone in the 2013 Super Bowl loss to the Baltimore Ravens?

“We’ll sit down with him, and if we see fit that he’s part of it, we’ll commit to that,” Lynch insisted.

Shanahan added that, in his playbook, there is no such thing as a one-size-fits-all quarterback. Before his two-year run with the slick-passing Ryan, he devised a Washington Redskins offense around Robert Griffin III. Kaepernick is a hybrid of the two – not the pure passer of a Ryan but a larger version of the nimble-footed Griffin.

“People have won in this league being pure throwers, making every throw in the pocket,” the coach reminded. “People have won in this league making plays with their legs. There have been tall quarterbacks who have made it; there have been short quarterbacks who have made it. There’s lots of ways to do it.”

The 49ers, who have the No. 2 pick in the upcoming NFL draft, have much to ponder and even more to prove. There is Lynch’s inexperience, Shanahan’s shaky Super Bowl play calling, Kaepernick’s demise and presumed departure. But it starts with Kaepernick. Do they give rehab another try or encourage him to find another home?

The Shanahan-Lynch era begins when that question is answered.

Ailene Voisin: 916-321-1208, @ailene_voisin

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