Power Ranking the 49ers’ Biggest Issues
All is not sunny in San Francisco.
It’s a testament to the cruel landscape of the NFL for the San Francisco 49ers to be sitting at 4-2 with three crucial wins over their division rivals, yet to still have a pessimistic outlook. Well, that is the case for Kyle Shanahan’s team that’s limping along near the top of the NFC. While the wins have added up, the issues remain prevalent.
The Young DBs
There was a lot of hype for some of the young defensive backs in the backfield rotation. Marques Sigle and Renardo Green stood out as players fans were hoping to take a step up, while Upton Stout was added in the third round as a rookie expected to see playing time.
It has been this regime’s M.O. to play it thin at secondary and rely on younger or lesser talent to fill in the gaps, whereas they dump resources into the front seven to maintain dominance up front and in return, help out the back end. This strategy has been largely successful for them, but the drawbacks have also been visible as the pass rush has struggled.
The ups and downs for all these players have been clear. As Deommodore Lenoir takes one side of the field away, it leaves the younger players vulnerable to be picked on. It doesn’t help that the pass rush post-Bosa has dried up, as they’re barely hanging on.
We’ll see how this group plays with the return of Malik Mustapha, another young player and coming off an injury. The depth won’t hurt, but one of the team’s healthiest units must step up in the absence of others.
The Run Game
The Kyle Shanahan scheme has boasted an excellent run game ever since his father became a prominent offensive mind back in the 90s. Well, through six games in 2025, the 49ers are 30th in rushing yards per game, ahead of only the Titans and Bengals.
Considering the offensive line is mostly made of hand-picked players and that Christian McCaffrey is healthy, it should be almost impossible to be that low amongst the league. This is the case, however, as McCaffrey only has one touchdown on the ground and has had more yards receiving than rushing in all but one game.
The bulk of the blame does seem to be on the offensive line; Trent Williams looks as human as he ever has, and Colton McKivitz is fine but not a needle mover. Playing through the tackles has been how this team has operated, but the lack of movement from the interior now greatly outweighs the positives from the tackles. Williams has still been a positive asset, but he alone can’t make this unit whole.
Dominick Puni appears to be playing hurt, but his sophomore slump certainly appears to be hurting the interior. This doesn’t seem like a problem that’ll go away, so it’ll be up to John Lynch and co. to finally address this unit with another difference maker next off-season.
Lack of Pass Rush
When Nick Bosa went down with an ACL injury, we knew the pass rush was going to suffer. Unfortunately, the early returns haven’t just been bad, they’ve been dire. Some of that can be attributed to replacing Bosa schematically, adjusting to a life without him. However, it’s clear that without a trade or addition, the pass rush just doesn’t have enough juice.
Because of their early wins, this group will get some time to gel. Mykel Williams, Bryce Huff, and even Jordan Elliott have shown flashes of excellence. Those flashes need to turn into some consistency soon if this team wants to compete into January.
It will also call on DC Robert Saleh to adapt to this situation. Historically a less blitz-happy scheme, Saleh prefers to save his pressure packages and confuse passers with his coverages. There’s very little room to stay in that space, as the young DBs and lack of pass rush are going to get killed if they can’t pressure the quarterback.
Injuries
It often feels like a cop out, because a majority of teams in the league are going through their share of injuries as well. What’s happening to the 49ers feels legitimately unfair and overwhelming.
They’ve done well enough playing through the Brock Purdy injury with Mac Jones. Losing George Kittle, Ricky Pearsall, and Jauan Jennings all at different times felt like a gut punch, but the offense has continued on. Losing Nick Bosa was brutal.
When Fred Warner went down on Sunday against the Buccaneers, it felt like a light went out.
The team is losing contributors left and right, but despite that they’ve been resilient and managed to beat the Rams in a massive upset shorthanded. Without Warner, there was simply not enough to work with to keep up against a NFC contender. The incredible run and conversion by Baker Mayfield highlighted a defense hanging on by a thread without Bosa or Warner.
Some reinforcements should be on the way. Purdy, Kittle and Pearsall are expected to return soon. Malik Mustapha came back last week to provide much needed depth and talent in the secondary. But, even if the team does get a little healthier down the stretch, they won’t be able to replace the impact Bosa and Warner provided.