Critiquing the coach: Where Kyle Shanahan must improve as a head coach

If you’ve been reading this website over the past two years, you’re well aware that I’m biased when it comes to San Francisco 49ers head coach Kyle Shanahan. He’s a mastermind play-caller that finds ways to motivate his players in unique ways. Shanahan takes the no-nonsense approach, which resonates with most players.

Last year, we had a series where we critiqued the coach. Today, we’ll put Shanahan under the microscope to see where he could improve. We’ll review defensive coordinator Robert Saleh later in the week.

There are several questions about Shanahan, the talent evaluator, and how well he coaches outside of calling plays. Most of the critiques you read about him are fair and often accurate. When Shanahan and John Lynch took over the 49ers roster in 2017, the best skill player on offense was...Torrey Smith? On defense, DeForest Buckner was in his second year, while NaVorro Bowman had suffered an Achilles injury the season prior.

It’s been an uphill battle since, and the team has done an impressive job of adding talent and personalities to help create a winning culture. Injuries have single-handedly ruined two of Shanahan’s four seasons. When Jimmy Garoppolo went down in 2018, that was supposed to be a learning year for Jimmy G. Fast forward two years, with the Niners having added a handful of impact players, and San Francisco now fields one of the best and deepest rosters in football.

But, injuries.

It’s OK to acknowledge specific struggles the team has this year and how those struggles are independent of injuries. What we haven’t done is discuss where Shanahan has struggled in 2020. Against the Saints, Patriots, and Rams, we saw the offense play with confidence from the opening snap and look like the 49ers of 2019. After the first few series, the offense’s success plummets, and Shanahan deserves some of that blame.

Critiquing the coach

It’s easy to second-guess decisions when they don’t work. Some of these decisions we are second-guessing should have never taken place, to begin with. Let’s talk about the play-calling and how Shanahan did not do his quarterback any favors on Sunday.

The 49ers had 15 first downs during the first half of the Saints game. They ran the ball on five of those plays. What’s the best way to help your quarterback build confidence and get him into a rhythm? By letting him throw the ball on early downs with easy completions. Eight times during the first half, the Niners offense faced 2nd & 7 or worse. When you get behind the sticks with a backup QB, your offense doesn’t have a chance.

Shanahan hasn’t trusted his quarterbacks all season. It’s clear as day. Everyone knows this. While it’s easy to pile on Nick Mullens, let’s remember that he was an undrafted free agent for a reason. There have been glimpses of success, but Mullens should not be a starter in this league. That can be true while also acknowledging Shanahan failed to help Mullens on Sunday.

On the second play of the game, after Jerick McKinnon was tackled in the backfield for a loss of three on first down, Shanahan dials up a slant route to Brandon Aiyuk, and Mullens finds him for a gain of 12. On 3rd & 4 later in the drive, there’s a crossing route with Richie James in a foot race over the middle. James is going to win that battle nine times out of ten.

Those are the throws Shanahan could use on early downs to help his quarterbacks moving forward. If Mullens isn’t seeing the field well or reading the defense, and he’s not, then simplify what he’s asked to do. Make your skill players do the heavy lifting. That didn’t happen on Sunday.

McKinnon had two targets on the afternoon. One came where he was lined up in the slot and beat Kwon Alexander for a gain of 13. The next two plays were a one-yard run on first down, a blitz where Mullens was hit, and a 3rd & 9 where the offense couldn’t convert. During 2019, Shanahan would run plays back-to-back several times a game if they were working. We haven’t seen that this year.

Stubborn Shanahan

If you know the running game isn’t successful, stop running the ball. Involving your backs in the passing game is an extension of the run, anyway. I mentioned all of the first down runs earlier and how it puts your QB at a disadvantage. The 49ers EPA per play on first and second down when they ran the ball Sunday was -0.47 with a success rate of 29%. When they threw the ball on early downs, their EPA per play was .06, with a 45% success rate. Only 5% of those runs resulted in a first down, while 33% of the passes went for first downs.

This was not an offensive line problem. And while Mullens could have thrown an interception, it was Shanahan being stubborn. Calling an A-gap run on 4th & 1 is not stubborn; it’s stupid. Everyone in the stadium knew that play was coming. New Orleans had six defenders lined up on the line of scrimmage. That play was similar to the 3rd & 5 wildcat play McKinnon ran a couple of weeks ago against Seattle. You are the head coach. Call timeout, and get your offense into a better situation.

Kyle is making the same mistakes in situations where he must improve. The game flow and making life easier on his quarterback are at the top of the list. There are plenty of fingers to point if you’re looking to blame someone for this season or the Saints’ loss. We could also question more of Shanahan’s decisions. Why are you rotating your right guards every other series? Why did it take two games to play Tarvarius Moore at safety? The politics in football are something that we’ll never be able to explain fully.

For a couple of weeks now, Shanahan has pointed to the Rams game at the end of this month. He feels like that’s when the team will get back a handful of starters. Fresh off a bye, we should see an offense that’s ten times as creative as we saw in New Orleans. Shanahan’s adjustments after the first couple of series haven’t happened during the past three games. Raheem Mostert and Deebo Samuel on the field should change that approach.

The injuries have been too much for the 49ers to overcome this season. Those should not be held over Shanahan’s head. This team has remained competitive, but special teams blunders against the Saints and big plays allowed during the previous two games have taken the Niners out of contention. After Sunday’s game, I asked Trent Williams how frustrating is it knowing that the offense hasn’t played complimentary football this season:

“As an offense, it sucks, man. We’ve had a revolving door at every position. Every week, we’re just mustering up enough guys to get on the field. From then on, we must establish a good gameplan. I felt like this gameplan was pretty sufficient when we had our plays and stayed ahead of the chains.

It’s just those couple of plays. Those turnovers in the red zone was really a killer. That gameplan blitz that they had, they had some success doing that.”

I put those slot blitzes on Mullens and Shanahan. Mullens has to see them coming. Shanahan is responsible for letting his young QB know they are. “Hey Nick, scan the field once you get to the line of scrimmage. If you see the slot cornerback staring through your soul, he’s probably going to blitz. Here’s the hot route.” Those same blitzes were killing the Niners running game as well. Here’s a stat: A Kyle Shanahan-led offense has run for 156 yards...in the past three games. That is not a typo.

Shanahan has proven to be a mastermind and the best play-caller in the NFL. He’s the head coach of the 49ers. Shanahan must evolve. We know what he can do with a stacked roster. Injuries happen to every team in the NFL. We need to see from Shanahan, a coach who can adjust after the first couple of drives when he’s not dealt four aces. A coach that’s willing to move off his tendencies, knowing that’s not what’s best for his offense in that specific moment.

Shanahan isn’t going anywhere, nor should he, as the 49ers coach helped turn around a franchise that was in the dumps and was a significant reason the offense had as much success as they did in 2019. On fourth downs this season, Shanahan has been much-improved from 2019. The 49ers are near the top of the league in fourth down decision-making. Shanahan must continue to evolve from a short-yardage, game-flow, and clock management perspective. I’m sure there are more.

Other teams and coaches have adjusted. Now it’s on you, Kyle.