49ers reportedly split on QB target for No. 3 pick
According to a recent report, head coach Kyle Shanahan is in disagreement with the Niners GM about which QB the team should select. Kyle Terada-USA TODAY Sports

The San Francisco 49ers made a bold move mortgaging the future to trade up for the No. 3 overall pick in the 2021 NFL Draft, determined to land a franchise quarterback they could build around. There are plenty of conflicting draft rumors about their target, and we now may know why.

During the predraft process, general manager John Lynch and head coach Kyle Shanahan have been busy evaluating their options. They both attended the Pro Day workout for Alabama quarterback Mac Jones, where at least a few bad throws didn’t make the strongest impression. San Francisco has also been tied heavily to North Dakota State star Trey Lance, a developmental prospect who could sit behind starter Jimmy Garoppolo in 2021.

There’s been plenty of debate about who the 49ers should draft with the No. 3 pick. Not only is that discussion taking place in mock drafts and across sports media, but it seems there is even deliberation in the 49ers’ organization.

NFL insider Michael Lombardi spoke to Sirius XM’s "The Rap with Patrick Meagher" (h/t NBC Sports) about the 49ers’ plans at quarterback. Not only did he add to the growing buzz surrounding Jones, but he also indicated there is some internal debate taking place in San Francisco.

“Someone told me yesterday — not an NFL head coach — but someone told me that there is a conversation in the building that Kyle wants X and maybe Lynch wants Y. Look, I’m going to be very clear here — Kyle is going to make this pick. It’s in his contract. It’s not a question of he’s just going to do it by his personality. The Shanahans run the 49ers. Lynch is there to do what he is told to do.” 

Obviously, Shanahan will get final say. While Lynch has the title that typically carries more authority, this organization has a history of giving greater power to the head coach. With this being Shanahan’s team and his offense, he will decide who is under center running the show for years to come.

What quarterback will the 49ers draft with the No. 3 pick?

One of the strongest points connecting Jones to the 49ers is Shanahan’s history with quarterbacks. He coached Kirk Cousins in Washington and badly wanted the 49ers to sign him before he joined the Minnesota Vikings. Furthermore, he was the play-caller when Matt Ryan’s stats made him one of the NFL’s most effective quarterbacks. While a bit of a different talent, Garoppolo is also in a similar mold.

But adaptation is also crucial for a head coach. Shanahan certainly learned a lot from his father, and it’s shaped the time of passers he wants running his scheme. But after an ugly loss to the Buffalo Bills, led by Josh Allen, Shanahan admitted he is seeing a change in the game and it can now be won in different ways with elite-type guys. He also made it clear he isn’t specifically looking for a Cousins-like quarterback at No. 3 overall.

It’s still very possible that Jones is drafted by the 49ers, there is a ton of smoke suggesting it will happen. But while Jones is a passer worthy of a first-round pick, his game is eerily similar to Cousins. That can work at a high level in the right offense, but it rarely translates to a team getting over the hump.

That’s why it shouldn’t surprise anyone if Lance or Justin Fields is the No. 3 pick. Either quarterback could sit behind Garoppolo for a year and then become the San Francisco 49ers star in 2022, operating a more explosive offense.

This article first appeared on Sportsnaut and was syndicated with permission.

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