Who will the 49ers take at No. 3? What they learned by passing on Mahomes

Kyle Shanahan spoke to local reporters after his introductory news conference as the 49ers head coach in 2017. In a moment away from the bright lights and television cameras, he was asked what he looks for in a franchise quarterback.

“If you aren’t an extremely talented thrower, which means it’s effortless, you don’t think about it, you don’t have to go all these quarterback gurus and work on your motion, you were born to throw,” Shanahan said. “If you don’t have that, it’s very hard to succeed in this league because you got to make some throws into tight windows, on time, with ball placement. It’s hard to get people wide open in this league.”

It was hardly an earth-shattering revelation. Shanahan’s ideal signal-caller, at the time, was one of the best natural throwers in the world who could place passes timely and accurately. Which led to the curious decision-making process leading into the 2017 draft.

Shanahan and his new partner atop San Francisco’s hierarchy, general manager John Lynch, went into their first draft with the plan to sign Shanahan’s former pupil, Kirk Cousins. (They didn’t get Cousins because they were surprised by Bill Belichick’s offer of Jimmy Garoppolo for a second-round pick just before the trade deadline). They wanted to build out the rest of the roster before inserting a franchise quarterback (Cousins) a year later. So they began the year with journeyman Brian Hoyer.

Missing Mahomes, Watson

That planning led to passing on Texas Tech’s Patrick Mahomes and Clemson’s Deshaun Watson when the 49ers traded back one spot to take Stanford defensive lineman Solomon Thomas with the No. 3 overall pick.

Mahomes and Watson, of course, went 10th and 12th, respectively, to the Chiefs and Texans, who both traded up to get them. Neither quarterback was considered a slam dunk at the time. They would have gone far earlier if they were. But they both went to teams coming off consecutive playoff berths, which helps explain their rapid ascents.

Passing on Mahomes could be one of Shanahan’s biggest mistakes. Mahomes, of course, beat the 49ers with a heroic effort in the Super Bowl three seasons later, which included a career-defining throw on a third-and-15 in the fourth quarter that swung the game and helped Mahomes win game MVP honors following a furious comeback.

Passing on Mahomes in the draft is particularly galling given what else Shanahan said after his introductory news conference, when he was expanding on what he looked for under center. Mahomes is one of the most talented passers in NFL history.

“You’re always looking for one of those seven throwers on the planet, whatever that number is. I’m guessing there’s only around seven,” Shanahan said in February 2017. “So you better not only be set on that, saying, ‘Hey, I need one of those seven guys.’

“I hope to get one of those seven guys, but if you don’t, you got to find other ways to win.”

49ers’ have picked a QB before

All of which paints the backdrop after three losing seasons and a Super Bowl appearance with San Francisco. The 49ers entering 2021 mortgaged their future to move up nine spots in the draft, sending three first-round picks and a 2022 third-round choice to the Dolphins for the No. 3 pick, and a shot to rectify passing on Mahomes and Watson.

Back to that first draft in ’17. Shanahan wound up landing a quarterback with pick No. 104, a late third-round selection acquired in a trade with the Vikings. Shanahan viewed C.J. Beathard as an easy player to project based on the offense he ran under Hawkeyes coach Kirk Ferentz.

It was a pro-style scheme that relied heavily on the running game and play action (the 49ers drafted another player as a fit for their system two rounds later in a blocking tight end named George Kittle).

Beathard (6-2, 215) was hardly a physical marvel. He could have been confused for a punter based on his build. But he made sense for Shanahan, who drafted fellow Big Ten quarterback Cousins with the No. 102 pick five years earlier. Shanahan was asked if he thought Beathard was comparable to Cousins given their similarities as prospects and the likelihood they would start their careers as backups.

“Yeah, I think that’s exactly how you see it,” Shanahan said. “Anytime you take someone you want to see the potential to develop someone. ... Anytime you’ve got a guy that’s fearless, I think he’s extremely intelligent, football means the world to him, he really works at it, he’s accurate and he can process and play the game very fast in the pocket, I think that gives you a chance to play in this league.”

The Beathard pick didn’t work out the same ways Cousins did. Cousins has earned a pair of big contracts to be the starter for the Minnesota Vikings and went to the playoffs in 2019. Beathard didn’t earn a second contract with San Francisco, despite the team’s need at quarterback, and signed with the Jacksonville Jaguars this offseason likely to compete as a backup to future No. 1 pick Trevor Lawrence.

Shanahan decided to draft Beathard without meeting him in person. He left those meetings up to quarterbacks coach Rich Scangarello, who’s back with the 49ers after recent stints with Philadelphia and Denver. The only quarterback Shanahan worked out in person in 2017 was North Carolina’s Mitchell Trubisky.

Shanahan refrained from going to pro days, save for Stanford’s 15 miles up the road, where he got an up-close look at Thomas. Shanahan didn’t even meet with Beathard at the scouting combine, he said.

He also said something notable in December right before playing Buffalo’s budding star quarterback, Josh Allen, known for his size, arm strength and mobility. Allen helped the Bills get to the AFC title game last season and finished second in MVP voting behind Aaron Rodgers.

“It was him with a number of other guys, guys I was hoping were going to come out earlier, but they didn’t and so we looked at guys more that year and next year we had Jimmy,” Shanahan said.

What to learn about Shanahan

So is there anything to learn from Shanahan’s handling of the first and only quarterback he’s drafted since coming to San Francisco?

That much is unclear. The 49ers are keeping things close to the vest despite the rampant speculation about their preference for Alabama’s Mac Jones, whom Shanahan and Lynch saw up close at a recent pro day. And according to a report from The Athletic, the 49ers are likely to watch a second pro day for Ohio State’s Justin Fields, who is the overwhelmingly preference for fans and free agent cornerback Richard Sherman.

The quarterback most similar to Beathard would be Jones, given their limited athletic traits. Fields and North Dakota State’s Trey Lance have a better shot at becoming “one of those seven throwers on the planet” Shanahan mentioned in 2017, given their natural talents.

If you’re connecting the offenses they played in college, Lance’s pre-snap work at the line of scrimmage and play action is most similar to Beathard.

According to ESPN’s Nick Wagoner, 30% of Lance’s snaps came from under center, compared to 6.3% and 1.9% for Fields and Jones, respectively. Additionally, 24.3% of Lance’s snaps came under center with play-action, a key aspect of Shanahan’s offense. Fields and Jones: 5.8% and 1.9%.

And of the quarterbacks most similar to Allen, Lance would fit that bill given his athleticism, running ability and arm strength. Accuracy was Allen’s biggest knock as a prospect while many have argued the same for Lance. They also both played at FCS schools. Allen went to Wyoming and faced similar questions to Lance regarding competition level.

No matter what happens when the pick is made April 29, the perception of what Shanahan wants in a quarterback is at a tipping point. He pushed back on the idea of only being infatuated with Cousins or quarterbacks of similar skill sets.

Shanahan will either take Jones, continuing the narrative he only wants a quarterback to operate his system and play within structure, or an athletic player like Fields or Lance to elevate his team in the same way Mahomes, Watson and Allen have since entering the league.

“(Cousins is) the only (quarterback) I’ve been associated with because people thought I was trying to bring him here, which I was at the time,” Shanahan said March 29 after making the trade.

“It’s not because that’s how you draw it up. If you’re going to draw it up, you’re going to draw the biggest, fastest, strongest and best quarterback in the pocket.”

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