Commentary: 49ers coach Kyle Shanahan’s problems involve the roster, rookies

San Francisco 49ers fans are angry about the state of the team following Sunday’s loss to the Arizona Cardinals, who were playing backup quarterback Colt McCoy, while Kyler Murray watched from the sideline with an ankle injury.

“I know we’re a 3-5 team right now,” head coach Kyle Shanahan said Monday on his weekly conference call. “I believe we should have a better team (than) that record, and I know that starts with me.”

Indeed, Shanahan is the head coach of an underperforming team. There are nine games remaining and San Francisco is just one game back of a playoff spot, even if a playoff game seems like a mountain range away. The team has games against current No. 7 seed Atlanta (4-4), Minnesota (3-5) and Seattle (3-5), which are ahead of them in the wild-card standings, so there is an opportunity to jump back into the mix with a hot streak down the stretch.

Not all is lost — yet, anyway.

The Press Democrat’s Inside the 49ers blog

But as the embarrassing losses mount, especially at home, where the 49ers haven’t won since Oct. 18, 2020, pressure will grow and some will call for Shanahan’s job. That’s just how the NFL works.

As disappointing as this season is, Shanahan isn’t going to be judged in job security terms by owner/CEO Jed York until he can determine if rookie Trey Lance will be a winning franchise quarterback. The team made it clear there was a long-term vision in mind when it invested three first-round picks in Lance, and the fruits of the move weren’t going to bloom until well beyond 2021.

What that left was an awkward needle to thread: contend with a quarterback, Jimmy Garoppolo, you’re trying to replace. It’s a strategy that has rarely worked in the NFL. Shanahan is finding out why firsthand.

It’s been argued here and elsewhere the quarterback situation created a season-long contradiction. But that’s not what this column is about. It’s about Shanahan’s mishandling of the rest of the roster.

To be sure, general manager John Lynch technically controls the offseason 90-man roster while Shanahan determines the 53-man roster heading into the season. But let’s be clear: Shanahan is Lynch’s boss. He’s the one who hired Lynch to be his GM, so Shanahan is ultimately responsible for all the personnel decisions. He’s the most important person in the building on the football side.

Which is where this season has gone wrong. It’s with the roster, not necessarily the X’s and O’s. The long-held belief that coaches shouldn’t have final say on personnel is shining through for Shanahan in his fifth season at the helm.

49ers draft picks

Let’s examine the draft and the picks made after the team traded up for Lance.

This 2021 draft class was an important one. The 49ers recently gave out top-of-the-market contracts to George Kittle, Trent Williams and Fred Warner, meaning they were going to need to find players on cheap deals to contribute, particularly with the pandemic causing the salary cap to drop substantially, all while Garoppolo is still making $26.4 million.

But the picks made in rounds 2 and 3 have given the team nothing to this point. Those were the rounds where the team previously found gems like Deebo Samuel and Warner (while drafting misses like Jalen Hurd and Dante Pettis, as well).

Guard Aaron Banks, tapped in the second round, hasn’t played a snap this season. Third-round pick Ambry Thomas, the cornerback from Michigan, has appeared in three games but hasn’t gotten a defensive snap since the season opener.

Running back Trey Sermon, a third-round pick from Ohio State, whom the team traded a pair of fourth-round picks to select, was inactive on Sunday in favor of Jeff Wilson Jr., who had no training camp and just three practices before Sunday’s game after tearing a meniscus in May.

Sermon was beaten out by sixth-round pick Elijah Mitchell, who has three 100-yard games this season. That seems justifiable. What’s less justifiable is the idea that Wilson is a better option than Sermon after just three light practices and no training camp.

Wilson didn’t play Sunday, for whatever that’s worth. But his elevation over Sermon doesn’t tell the world Shanahan has all that much confidence in Sermon, who had 89 yards on 19 carries during the Oct. 3 loss to the Seahawks when Mitchell was out with a shoulder injury.

“We didn’t bring him here to come and start at running back. We needed to add some depth,” Shanahan said of Sermon. “He’s kind of been the odd man out, which is tough on him. It doesn’t mean that we don’t believe in him. He’s just not ahead of those other guys right now in terms of running the ball on first and second down.”

Back to Banks.

Right guard Daniel Brunskill is ranked 46th by Pro Football Focus in pass blocking among guards who have played at least half their team’s snaps. In run blocking, he ranks 29th. He’s an average player at best, but also clearly the team’s worst starting offensive lineman. The 49ers made it clear they wanted to replace Brunskill when they used the 48th overall pick on Banks, especially since highly drafted guards often have significant roles right away.

But Banks can’t. He suffered a shoulder injury during the preseason and has only been active for one game this season. Brunskill, meanwhile, allowed two sacks against the Cardinals on Sunday. Maybe a change is coming soon.

“I think he’s had his best couple weeks here lately and he’s starting to push (Brunskill) a little bit,” Shanahan said. “When that time is right for him and our team, we’ll make that move.”

On cornerbacks Thomas and fifth-round pick Deommodore Lenoir, Shanahan made it clear: He doesn’t think they’re ready to contribute.

“We weren’t bringing any of them here, we felt, to start,” Shanahan said. “We were hoping they could add some depth and be guys who could play on our team, and possibly do that next year.”

Both were given chances to play early in the season when starter Jason Verrett was lost to an ACL tear (yes, the same Jason Verrett who previously tore his ACL and Achilles, and was made the team’s top cornerback option this offseason after not re-signing Richard Sherman).

“And, unfortunately, they weren’t totally ready for it,” Shanahan said. “Yeah, I wish they were. But third-round pick and the fifth-round pick, they weren’t, and that’s why we’ve gone with some veterans instead of them, trying to get them some time to get to where they need to be.”

The handling of Thomas and Lenoir might be the hardest to reconcile, because the veterans the team brought in, Josh Norman and Dre Kirkpatrick, have proven to be bad options.

Norman played himself off the field on Sunday after getting an inexplicable taunting penalty while Kirkpatrick has been the defender responsible for two of the most embarrassing moments for the defense this season: the fourth-quarter touchdown when he was in “coverage” against Colts receiver Michael Pittman earlier this month, and Eno Benjamin’s touchdown run in the second half on Sunday when Kirkpatrick was dropped with a shoulder to the chest by the former seventh-round draft pick.

Which speaks to a bad process that Shanahan, as the head honcho, is responsible for. Either Banks, Sermon, Thomas and Lenoir were bad picks or they’re not getting developed properly — or both. Because Norman and/or Kirkpatrick have not proven to be winning options. Brunskill is hardly above replacement level. Wilson, coming off an injury, is somehow more playable than Sermon, who has been practicing since training camp began.

Maybe that changes as the season goes on. But for now, the team doesn’t have the depth at those key spots needed to contend.

That’s being proven in the win and loss columns.