Top Five Uncertainties the 49ers will Face in 2020

This article assumes the games will happen.

The top uncertainty facing every NFL team this year is the pandemic. Duh. We don’t even know if teams will play games.

This article assumes the games will happen. So here are the top-five non-Covid-related uncertainties the 49ers face in 2020:

1. The Young Wide Receivers

The 49ers had the same concern last year. They entered the 2019 training camp with a bunch of young wide outs, and hoped a couple would emerge as quality starters. The 49ers expected Dante Pettis to emerge as their No. 1 receiver -- remember that? He had just come off a strong second half of his rookie season.

But he came into last year’s training camp out of shape, according to the 49ers, and had a miserable season. So the 49ers added veteran Emmanuel Sanders at the trade deadline -- they probably wouldn’t have made it to the Super Bowl without him.

Now the 49ers have a slightly different group of young wide outs. Deebo Samuel is supposed to be the No. 1 receiver this year, because he played so well the second half of last season. But now he has a broken foot, and will miss training camp, preseason and probably a month of the regular season, too. What kind of shape will he be in when he returns?

If Samuel has a slow return from his injury, the 49ers might feel compelled to make another deadline trade for a wide receiver -- perhaps Bengals seven-time Pro Bowl wide receiver A.J. Green. He reportedly is unhappy in Cincinnati, and will be a free agent in 2021. If the 49ers acquire him at the deadline, they’d have to pay him less than $10 million in 2020, meaning they can afford him. They currently have more than $12 million in cap space. The Chiefs, for comparison, have $177 of cap space.

2. Jimmy Garoppolo’s Progress

The 49ers hope Garoppolo will make big strides during his second full season as a starting quarterback. Matt Ryan won an MVP during his second season playing for Kyle Shanahan.

But Ryan had a full offseason to prepare. Garoppolo has had no OTAs or minicamp. He has no Emmanuel Sanders, and no Deebo Samuel for a while, and very very little time to build rapport with the other young receivers.

Hard to expect Garoppolo to play the best football of his career under these conditions, although he still may.

3. The Defensive Backs

Sure, the 49ers defense ranked No. 1 against the pass last season. But it ranked No. 1 mostly because of its great defensive line. The secondary still is the weakest link of the defense, if not the entire team.

The best player in the secondary, Richard Sherman, turned 32 this offseason. He’s old for a defensive back, and his play began to slip in the playoffs.

Then the 49ers have safeties Jimmie Ward and Jaquiski Tartt. They’re good, but miss lots of games. Tartt never has played a full 16-game season in his career, and Ward hasn’t played one since 2015. If either one suffers an injury, the 49ers might feel even more compelled to trade for Jets All Pro safety Jamal Adams. The 49ers have shown interest in Adams already, according to multiple reports. He would make them instant Super Bowl favorites.

4. Javon Kinlaw’s Knee

Kinlaw didn’t fail any physicals at the NFL Scouting Combine, but teams flagged his knee as being “at risk for arthritis” -- similar to 49ers defensive end Dee Ford.

Last season, Ford started only two games and played just 226 snaps because he had severe tendinitis in his knee. He missed lots of practices and had to split time with other players during games just to be effective.

Will Kinlaw have to split time, too?

The 49ers drafted Kinlaw to replace DeForest Buckner, who rarely came off the field. But he didn’t have an arthritic knee. Kinlaw might be most effective as a pass-rushing specialist who splits time with a run-stuffing specialist. Otherwise, the 49ers might wear down Kinlaw’s already worn-down knee.

5. John Lynch’s Future

For the first two and a half years of his tenure as 49ers general manager, Lynch was the face and voice of the organization. He spoke and tweeted about the 49ers quite often.

But he has gone relatively silent the past two months. Hasn’t tweeted since May 23 or spoken to the media since April. Hasn’t addressed Shanahan’s extension or Samuel’s broken foot or anything at all. Highly unusual for him. And highly mysterious.

Let’s recap Lynch’s past 12 months and look for clues.

Last year after the draft, Bleacher Report’s Matt Miller reported there was “friction” between Lynch and Shanahan:

“According to sources in the team's scouting and coaching staff, the two aren't in lockstep as far as the vision of the offseason and the future of the franchise. The coach, Shanahan, wants to scheme and develop players while not being bothered with the player evaluation process, but more and more he finds himself involved while not trusting the decision-making of Lynch—a former media analyst after his Hall of Fame playing days but not someone with a scouting background.”

This year, the 49ers 2020 draft seemed like more of a Shanahan production. The trade up in Round 1 for wide receiver Brandon Aiyuk had Shanahan’s fingerprints all over it. Shanahan said Aiyuk was his favorite wide receiver in the entire draft. Lynch said he worried at the time that trading up for Aiyuk would prevent the 49ers from acquiring Trent Williams. He was wrong. They got Williams anyway.

Since the draft, Lynch has posted just six tweets, and none have them have addressed the 49ers’ official account directly. And he has given zero press conferences since he went on KNBR in San Francisco on April 30 essentially to say George Kittle needs to lower his contract demands. And Lynch has received no contract extension of his own, even though the 49ers gave one to Shanahan.

Do the 49ers still have a general manager?

Is Lynch still working on extending Kittle’s contract, or extending his own? Or is Lynch trying to get out of his contract and go back to broadcasting?

What is going on? And why the mystery?

I imagine we’ll find out soon enough.