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Kyle Shanahan made a classic rookie coaching mistake. But before I get into that, I want to praise him.

Some of the moves he has made this offseason were good.

Starting with the players he released, or chose not to retain. Along with rookie general manager John Lynch, Shanahan was ruthless. He cut Torrey Smith, the 49ers’ blockbuster free-agent signing from just two years ago and the third-highest-paid player on the team. He was getting worse and had no place in the 49ers future. Goodbye, Torrey, more bust than blockbuster.

Shanahan also cut Antoine Bethea — a Pro Bowler in 2014 — and Marcus Martin — a former third-round pick. Goodbye, Antoine and Marcus. You don’t fit the new 49ers’ schemes.

And goodbye, Colin Kaepernick. Reports indicate Shanahan would have cut him if Kaepernick hadn’t opted out of his contract. No sentimentality for the quarterback who took the 49ers to the Super Bowl in 2013. I admire Shanahan for focusing on the future.

I also admire how active and aggressive he has been during free agency. The previous general manager, Trent Baalke, who was awful, typically waited until the second wave of free agency to sign second-rate players on discount. Shanahan signed eight players before free agency even officially began.

Shanahan signed nickel back K’Waun Williams, nose tackle Earl Mitchell, linebacker Malcolm Smith, quarterback Brian Hoyer, fullback Kyle Juszczyk, tight end Logan Paulsen and wide receivers Marquise Goodwin and Pierre Garçon.

Last year, Baalke signed only two free agents — Zane Beadles and Thad Lewis — even though the 49ers were coming off a five-win season and had almost $50 million in cap space. Baalke essentially promised the fans the Niners would stink last season, and stink they did.

Shanahan is giving fans a reason to be excited for 2017. He’s making moves which suggest he thinks the team can be competitive right now — or at least watchable. I admire his confidence.

I like two of his signings in particular — Juszczyk and Hoyer. Juszczyk is a 25-year-old Pro Bowl fullback who can play tight end as well. He caught 78 passes for the Baltimore Ravens the past two seasons. He will be a key player for the 49ers in the present and future.

Hoyer is not someone who figures into the team’s future, but he’s important for 2016 and here’s why.

Hoyer played under Shanahan in 2014 when Shanahan was the offensive coordinator for the Cleveland Browns. Hoyer knows Shanahan’s system and offensive terminology. Hoyer can serve as a quarterback-caddy for the starting quarterback Shanahan signs or drafts this year, whoever he may be.

Hoyer can help the starter learn the playbook, show him what to do during quarterback meetings and tell him how to adjust to Shanahan’s coaching style.

Or, Hoyer can be the starting quarterback himself in 2017 and give Shanahan the option to wait until 2018 to draft a rookie replacement. Hoyer gives Shanahan flexibility.

Smart signing.

Now it’s time to talk about Shanahan’s rookie mistake, and it’s a big one. I downplay Lynch because this is Shanahan’s team.

Shanahan paid a premium for free agents he’s comfortable and familiar with. Six of the eight players he signed have played for Shanahan or one of his assistant coaches.

What did Shanahan get by paying for comfort and familiarity? Maybe five or six wins next season, plus a bunch of veterans who won’t factor into the team’s long-term plans.

Shanahan is in the first year of a six-year contract. He has at least one grace-period season to rebuild a roster that was decimated by early retirements, draft busts and medical redshirts who never panned out. The Niners roster is Swiss cheese.

When building a team from scratch, the idea is to bring in young players who will be here for the long haul, players who can become major contributors during Years Two, Three, Four, Five and Six. Shanahan is not doing that.

The Dallas Cowboys from the late 1980s and early 1990s created the classic template for restocking a barren roster. They spent first-round draft picks on Michael Irvin, Troy Aikman and Emmitt Smith in consecutive years and played each of them as rookies. That team endured a 1-15 season in 1989 as those players learned on the field. The Cowboys accelerated their development. Then, the Cowboys won three Super Bowls a few seasons later.

Shanahan’s veteran signings only delay the development of young players who could contribute in the future. Shanahan is wasting time. Rookie mistake.

He gave a five-year, $26.5 million contract to linebacker Malcolm Smith who turns 28 in July and got exposed as a liability in pass coverage and run support while he was with Raiders the past two seasons. They didn’t want him anymore. But the Niners want him because their new defensive coordinator, Robert Saleh, knows Smith from their days with the Seattle Seahawks. Bad thinking.

Shanahan also gave big money to Pierre Garçon, who will be 31 next season and is slowing down. He will earn $23 million from the 49ers during the first two years of a three-year contract.

No other team would have given Garçon anywhere near that amount of money. The Niners had almost zero competition for him. And yet Shanahan overpaid, simply because he coached Garçon in Washington and knows him well. That’s a bad reason to overpay anyone, especially an old wide receiver.

Garçon probably won’t even be on the 49ers’ roster if and when they’re good a few years from now. He will be retired. The Niners just gave him his 401(k) plan.

Instead of signing Garçon, Shanahan should have signed Kenny Britt, who is only 28 and still has fresh legs and a future in the NFL. Britt ended up signing with a worse team, the Cleveland Browns, for $8 million per season.

Britt is better and cheaper than Garçon. Why didn’t the Niners court Britt? Probably because Britt doesn’t know Shanahan’s system and Shanahan would have had to teach it to him. And that probably makes Shanahan uncomfortable.

Comfort shouldn’t matter when you’re coming off a 2-14 season. Comfort is overrated.

Longevity is what counts.

Classic rookie coach mistake.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat’s website. You can reach him at grantcohn@gmail.com.

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