The 49ers biggest strength and weakness after three games

We asked Twitter what the San Francisco 49ers’ biggest strength is as a team after three games. Quite a few of you said the schedule, which is logical and tough to disagree with. The 49ers are fortunate to have played both New York teams early in the season as the Niners have battled injury. Could you imagine if San Francisco started the season with a divisional opponent and had to follow that game up with two playoff teams? That would’ve put the team behind the 8-ball, and likely cost them a shot at the playoffs.

Depth was another popular answer, and how could you not answer that? The depth on the 49ers has been tested in ways the front office couldn’t have imagined. If you were to ask general manager John Lynch where he thought the team would be if Dontae Johnson were playing starter snaps in Week 3, I imagine he wouldn’t have been too pleased. Yet, here we are, 2-1 after three games.

There were a few head-scratching answers. Some say the running game, which we’ll get to later. So far, I love the team’s resiliency and preparation, which is why the Niners’ strength is obvious to me.

Coaching

When you beat an NFL team by nearly four touchdowns with primarily your backups playing, that says more about you than it does the team you beat. It wasn’t just the way the 49ers beat the Giants; it was in the manner of how they did. I will forever nitpick Kyle Shanahan’s decisions because he’s on a pedestal that few others are. So when you’re running the ball on first down over and over again when it’s much easier to throw the ball on early downs, especially with play-action, fans have every right to be upset.

That shouldn’t take away from Shanahan or Robert Saleh’s brilliance. The 49ers are the only team in the NFL that are in the top-eight in DVOA in both offense and defense. That says a lot as DVOA adjusts for the opponent. We covered how RPOs helped Nick Mullens against the Giants on Tuesday. The only quarterback who had a higher EPA per play during Week 3 than Mullens was some Patrick Mahomes guy. Mullens was fourth in success rate as well. That’s Kyle putting his quarterback in a great position to succeed. Yes, it was against New York, but the 49ers were without their top everything on offense, but still executed. They were 8 of 12 on third downs and scored touchdowns on four of their six red zone drives.

That’s all Shanahan.

On the other side of the ball, Saleh is adapting to life without Nick Bosa and Dee Ford quite well. New York never reached the red zone this past Sunday. I love the idea of blitzing young quarterbacks as there aren’t many repercussions since they don’t see the field well. Usually, younger quarterbacks panic when they see pressure and make mistakes. Saleh blitzed Daniel Jones 31% of the time. That’s 11% higher than the 49ers blitz rate in 2019. The defense has plenty of speed and blitzing puts them in an aggressive, attacking mindset that makes them play better. It wasn’t against good teams, but the 49ers stifled their opponent, and that’s all you can ask.

It’s promising knowing that San Francisco will be prepared on both sides of the ball heading into every game.

Biggest weakness

So, about that running game. The offense is having success in spite of the line, which ranks 31st in adjusted line yards. The team’s calling card is supposed to be running wide zone. This year, the 49ers are 23rd in adjusted line yards behind the left tackle and 31st when running behind the right tackle. I’m not a fan of ESPN’s pass/run-block win-rate, as it’s calculated by using chips in players’ shoulder pads and has proven to be a bit fluky. In their stat, the 49ers are winning 55% of the time against the pass, which is 23rd, and 65% against the run, which is 29th. A Kyle Shanahan-led offense is struggling mightily to run the ball.

Some fans may think the 49ers running game is fine thanks to some explosive runs from Raheem Mostert. Outside of the back-to-back rushes from Jerick McKinnon on Sunday that went for 10 and 11 yards, the running game did a whole lot of nothing. The 49ers are 13th in rushing EPA, which factors in those long rushes. On a down-to-down basis, which is more telling, the 49ers are 25th in success rate on the season.

I’m stumped as to what the issues are. It’s not as if it’s one person. Everyone is missing blocks. Shanahan isn’t running one scheme, either. He’s changing up the run plays and personnel but to no avail. The reason I’m worried is that eventually, the 49ers will be forced off their game script. They won’t be playing with the lead or in favorable conditions. What happens when you’re playing a quality opponent? We are going to find out soon enough. San Francisco has to figure out what’s going on with the five guys upfront. They’re a problem after three games.