49ers enter 2024 season with legit concerns amid Super Bowl aspirations; last chance at title run?

This is the eighth installation of Thursday Thoughts, a series that looks at key topics across the NFL landscape. After we've waited and waited and waited for some clarity, the time has come to assess where the San Francisco 49ers stand, now and in the future.

The offseason and preseason, usually, are times for joy. This guy is in the best shape of his life ... This guy lost bad weight ... This guy gained good weight ... This guy has a new diet ... This guy is back from injury and looking better than ever ... This guy is ready to break out ... The possibilities are endless when there's a zero in the loss column.

When it comes to the 49ers, though, things aren't so peachy. This guy (Christian McCaffrey) is dealing with a calf strain and has barely practiced. These guys (Brandon Aiyuk and Trent Williams) are also not practicing because they're unhappy with their contracts, and that has meant this guy (Brock Purdy) has had a less-than-fun preseason without his normally excellent support system.

It's not just the biggest names. These guys (linebacker Dre Greenlaw and cornerback Ambry Thomas) won't be back until well into the season. Another guy (guard Aaron Banks) is in a race to be ready for Week 1 after breaking his pinkie. These guys (offseason edge-rusher additions Leonard Floyd and Yetur Gross-Matos) suffered knee injuries -- albeit minor -- on back-to-back preseason plays, and that's already with another guy at the position (Drake Jackson) done for the season.

Every team deals with injuries, and one could argue bumps and bruises happening now is better than them happening later.

But not every team deals what the 49ers are dealing with regarding Aiyuk and Williams, and dealing with it right now -- with the 49ers right in a Super Bowl window they've been oh-so-close to breaking through -- is close to the worst-case scenario.

The Aiyuk quandary has persisted for months, well before he requested a trade in mid-July. There have been times where a trade seemed imminent -- the Patriots reportedly met both the 49ers' trade demands and Aiyuk's contractual demands, but nothing came of it -- and times when San Francisco had real momentum.

Both general manager John Lynch and head coach Kyle Shanahan had their most pointed words on the situation Wednesday, with Shanahan saying Aiyuk was medically cleared and therefore expected to practice, and Lynch saying, "At some point, you've got to play."

Aiyuk didn't practice. 

It's been an offseason that has seen the wide receiver market explode. Each of the top-six highest-paid wide receivers on average annual value signed deals this offseason, and each is making north of $28 million. Aiyuk, playing on the fifth year of his rookie deal, is due just over $14 million.

There's no doubt he's worth more than that. Aiyuk is coming off a second-team All-Pro season in which he caught 75 passes for 1,342 yards. Only George Pickens averaged more yards per reception than Aiyuk's 17.9. His vertical abilities added an element that made an already-outstanding offense historically good. Then add in the blocking, no small aspect in this offense. Aiyuk earned Pro Football Focus' fifth-highest run-blocking grade among wide receivers. It's already hard to find a wide receiver as good in the passing game as Aiyuk who is also willing to block. But Aiyuk is more than willing. He is excellent.

Williams, meanwhile, has been the pinnacle of blocking prowess. In four years with the 49ers, he has ranked first, first, first and second in PFF's yearly tackle grades. Even at 36, he is an overwhelming force. He's No. 3 in Pete Prisco's 2024 Top 100 players list. Over the last two seasons, no team has rushed for more yards or more yards before first contact when rushing behind their left tackle than the 49ers.

Unlike Aiyuk, Williams is among the highest-paid players at his position, thanks to a six-year, $130-million contract that began in 2021. Like Aiyuk, though, there's not much security. San Francisco can get out of Williams' contract after this season. His $22 million and $32 million salaries in 2025 and 2026, respectively, aren't guaranteed. Williams is reportedly willing to sit out the start of the season, and there's precedent here: He held out until late October in 2019 with Washington.

There's no doubt Shanahan runs a terrific system, but there's also no doubt he has terrific players to help. Neither can thrive without the other. Any potential Aiyuk and/or Williams absence(s) would, therefore, be an issue.

Those second and fourth lines are a bit more advanced and all-encompassing than the first and third, so I'll put it to you this way: Using expected points added per play ...

• The number with Aiyuk and Williams on the field would have been best in the NFL. The 49ers overall led the league in this category, after all.
• The number with at least one off the field would have been 10th, similar to the Seahawks.
• The number with both off would have been 29th, slightly worse than the Steelers.

Rest assured the drop-offs wouldn't be as steep this year. Shanahan is a premier offensive mind (if not the premier offensive mind) in the NFL, and the 49ers drafted Ricky Pearsall in the first round. They would adjust. There's too much talent on the staff and the roster. But SportsLine projects significant drop off if Aiyuk were to leave. And it's no coincidence that the two games Williams missed -- against the Vikings and Bengals -- and the game he missed much of (Ravens) were among the offense's worst performances and resulted in three of the 49ers' five losses all season.

The 49ers simply can't afford for this to be a wasted year. No team has won more regular-season games over the past two seasons, and only the Chiefs have won more playoff games over the past five. There are age concerns with Williams, Floyd, George Kittle and Javon Hargrave all on the wrong side of 30, and McCaffrey and Deebo Samuel -- premier, rugged playmakers with injury pasts -- both 28. It's not going to get better than this.

But more so, this is the last year Purdy is cheap. He costs a hair over $1 million against the cap. He's the cheapest quarterback on his own team, behind backups Joshua Dobbs and Brandon Allen. In terms of cash spent, the 49ers have the second-cheapest quarterback room in the NFL, which allows them to have the most expensive running backs and defensive linemen, the third-most expensive wide receivers and the sixth-most expensive tight ends, according to Spotrac. Former Mr. Irrelevant becoming a starting quarterback at all, much less one leading a historically efficient offense while playing for ridiculously cheap, is a miracle.

But the 49ers are going to have to pay Purdy next season, when they have many free agents-to-be. To start, there's Greenlaw, Charvarius Ward, Deommodore Lenoir and Talanoa Hufanga, the latter two having vastly outperformed their contracts. If they can't get a contract or trade done, Aiyuk joins that list as well. That's with tons of of money committed to the positions listed in the last paragraph. There are very, very tough decisions that must be made, and that's what makes this year so, so important.

Perhaps the best comparison is the team that has stood in the 49ers' way twice: the Chiefs. Patrick Mahomes led them past the 49ers for Super Bowl LIV when he was still on his rookie deal. He got a monster deal months later, and the Chiefs had to make similar tough decisions. Sammy Watkins and Eric Fisher were off the team by the end of the 2020 season. Frank Clark, Tyreek Hill, Tyrann Mathieu and Anthony Hitchens -- the four largest cap hits on the 2021 team -- were all gone shortly thereafter. Orlando Brown Jr. departed last offseason for the Bengals.

The biggest difference, of course, is Mahomes. The Chiefs offense was nothing special last year, and yet in the crucial moments, it was Mahomes and Mahomes only. It's always Mahomes. If it weren't for him, we're talking about the 49ers very differently. While Purdy has been a revelation, he's not Mahomes. The very supporting cast Purdy's likely to lose -- in a similar manner to how Mahomes lost his -- currently elevates Purdy significantly. How he would perform without it is a question. Meanwhile, we've seen how Mahomes dealt with his worst supporting cast. He won a Super Bowl.

The Chiefs have also done a terrific job drafting to replace lost parts. Several cheap, home-grown defenders (L'Jarius Sneed, Trent McDuffie George Karlaftis, Willie Gay Jr., Nick Bolton, Michael Danna, Juan Thornhill) blossomed into solid starters, and Sneed and McDuffie became stars. Defensive coordinator Steve Spagnuolo has been outstanding. Last year's offense featured Pro Bowler Creed Humphrey, Trey Smith, Isiah Pacheco and Rashee Rice, all drafted and developed by Kansas City.

The same can't be said for the 49ers. The 2021 class, infamously led by Trey Lance, had some hits late, which has already served as a boon. But as Josh Lubow of the AP pointed out, Purdy is the saving grace for the 2022 draft.

In 2023, the 49ers didn't have a pick until the third round, and the early returns on that class weren't particularly notable. San Francisco projects to start six players it has drafted since 2021. Kansas City will likely double that. Put it all together -- the quarterbacks, the drafting, the fact that one franchise has three Super Bowl trophies in the last five years and the other has zero -- and you see why Kansas City's dynasty feels endless while San Francisco's juggernaut, in the moment, feels unsteady.

Outside of the Aiyuk and Williams situations, the 49ers have rightfully operated as a team with Super Bowl aspirations should. They brought back Jauan Jennings, a Super Bowl standout who does all the invaluable dirty work. They beefed up the defensive line and edge units, added secondary depth and changed coordinators after the defense quietly slipped from elite to just good (and, in some areas, not even good). They drafted a first-round wide receiver and a third-round guard who could start. With Williams and Aiyuk, there is no reason to doubt them as a bona fide top-tier contender.

But without Aiyuk and/or Williams, those hopes take a substantial hit. In a year with so much riding on it, that's a risk the 49ers don't want to take, but it's one they're getting closer and closer to taking every day.

More Thursday Thoughts:
Part 1: Can Caleb Williams and the Bears deliver on high expectations?
Part 2: Is this the Cowboys' last run as we know them?
Part 3: How will quarterbacks returning from season-ending injuries fare?
Part 4: What happens in the AFC North, the league's best and most intriguing conference?
Part 5: Is it the new-look Bills' time to break through?
Part 6: How will big-name running backs impact their new teams?
Part 7: Which young quarterbacks will take their teams to the next level?