McDonald: Kyle Shanahan missed on Mahomes. We still don’t know if he can develop a star 49ers QB

SANTA CLARA — The NFL’s gold standard as it applies to quarterbacks visits Levi’s Stadium Sunday, serving as a reminder that after more than five years, we have no idea if 49ers coach Kyle Shanahan has the capability to draft, acquire or develop a championship-level player at the most important position in professional sports.

With the 49ers at 3-3 going into their game against the Kansas City Chiefs, Shanahan was concerned enough to authorize a blockbuster trade for running back Christian McCaffrey to help make up the difference.

Shanahan and others whiffed on Patrick Mahomes in 2017. Andy Reid of the Kansas City Chiefs knew what he was looking at and traded the No. 27 pick in the first round, a third-round pick and a first-rounder in 2018 to get him at No. 10. The 49ers had their shot at Mahomes at No. 3 after trading back one slot but instead went with defensive end Solomon Thomas.

Mahomes was in his third year when he engineered a 31-20 come-from-behind win over the 49ers in Super Bowl LIV in Miami following the 2019 season.

Whatever doubt Shanahan had about Mahomes during his first draft as head coach ended in the Super Bowl, and the 49ers understand what they’re up against in Sunday’s return engagement against the Chiefs, who are 4-2 and a factor every year under Reid.

“He’s not much different,” Shanahan said Wednesday. “Just been in a lot more situations, more experience. He was unbelievable then and he’s unbelievable now.”

In part because the 49ers don’t have a quarterback Shanahan trusts to dominate as Mahomes does, he traded a cache of draft picks to Carolina Thursday to acquire McCaffrey, the former Stanford star and one of only three running backs to have 1,000 yards rushing and 1,000 yards receiving in the same season.

Dealing for a running back to compensate for issues at quarterback is not the usual M.O. for the 49ers or anyone else. But the 49ers are all-in, and Jimmy Garoppolo needs help.

Shanahan traded for McCaffrey because he still hasn’t found his Joe Montana or Steve Young, let alone Mahomes. After a history of safe, programmable quarterbacks, Shanahan stepped out of his comfort zone to trade up and get Trey Lance at No. 3 overall in 2021. It backfired when Lance, who like Mahomes was mostly a spectator as a rookie, broke his right fibula in Week 2.

So the 49ers are getting by with the serviceable Garoppolo, on whom the 49ers  bestowed a five-year, $137.5 million contract as a reward for winning five low-pressure games at the end of a lost season in 2017 that began 0-10.

We don’t know how good Lance would have been this year, although it’s fairly certain he wasn’t going to throw 50 touchdown passes and win the MVP in his first year as a starter as Mahomes did in 2018.

Nor do we know if McCaffrey will be what the 49ers need to make a run at the Super Bowl. One thing is certain — the deal would never have been made if the 49ers felt they had the quarterback to take them to the land of Montana and Young.

So we wait and wonder if Shanahan can ever mold a championship quarterback to a system as Bill Walsh did.

NFL teams are built from quarterbacks down, not running backs down. Since Shanahan is in his sixth season, with the 49ers committed to him through 2025 after a contract extension, it’s hard to give him the benefit of the doubt in that area.

Included among quarterbacks Shanahan has trained before becoming a head coach are Matt Schaub with Houston, Donovan McNabb, Rex Grossman, Robert Griffin III and Kirk Cousins in Washington, Brian Hoyer in Cleveland and Matt Ryan in Atlanta.

The most dynamic talent was Griffin, who passed for 3,200 yards with 20 touchdown passes and five interceptions as the No. 2 overall pick out of Baylor and rushed for 815 yards. And you could make the argument that Mike Shanahan, Kyle’s father and Washington’s head coach, was the one who did the heavy lifting with Griffin, who was never the same after a knee injury late in that first season.

Ryan was already established as a top-tier quarterback, and he took to Kyle Shanahan’s system in the second year to win an MVP in a season during which Atlanta won the NFC Championship.

As good as he was, Ryan was in Shanahan’s wheelhouse as a talent, someone who could execute the coach’s wishes without getting too bold, operating a preferably run-oriented offense heavy with outside zone scheme.

There were actually two quarterbacks coming out in 2018 who could push the boundaries of an offense — Mahomes of Texas Tech and Deshaun Watson of Clemson. Shanahan took a pass because he had his eyes on Cousins, with whom he’d worked in Washington.

Passing on Watson, who went No. 12 to Houston, looks good in hindsight given the sexual misconduct allegations that currently have him serving an 11-game suspension. But passing on Mahomes because you might be able to get Cousins in free agency?

This is how Shanahan broke it down in the days preceding Super Bowl LIV between the 49ers and the Chiefs:

“Mahomes was a freak. Could make any throw. Had the ability to do anything . . . it’s pretty well documented the relationship I had with Kirk being in Washington and I felt very confident he wasn’t going to stay there. Anytime you go into a season knowing that a franchise quarterback was going to be available, it made me a lot more picky with what we were looking at.”

So the picky 49ers traded back a spot and made Thomas the No. 3 pick in the draft and then got linebacker Reuben Foster at No. 31. Lynch said in the week preceding his Hall of Fame induction that he was at Mahomes’ Pro Day and was blown away by his talent but that his attendance in Lubbock was mostly a “smokescreen.” As it turned out, the 49ers could have gotten him as low as No. 9, although they never bothered to find out.

Cousins, who signed with the Vikings in 2018, might not be among the top 10 quarterbacks in the NFL. He never became a 49er after Garoppolo became available via trade with New England in 2017. Like Cousins, Garoppolo is stable and safe, someone Shanahan can trust to operate his offense and not go off-script.

Before Garoppolo arrived, Shanahan’s quarterbacks in his first season with the 49ers were Hoyer, with whom he’d worked as Cleveland’s offensive coordinator in 2014, and C.J. Beathard. Beathard was considered a reach in the third round of the Mahomes-Watson draft. Both were game managers at best and something less than that for the 49ers given their supporting cast.

Even when Shanahan took Lance, he was also considering Mac Jones, a game manager who thrived at Alabama because of surrounding talent.

Contrast Shanahan’s methods with how Reid has developed Mahomes. Reid has smoothed out the rough edges while at the same time allowing for Mahomes to go off schedule and make something out of nothing with spontaneous brilliance that can’t be accounted for in a playbook.