Without question, the biggest draft mistake committed by Kyle Shanahan and John Lynch throughout their tenure with the 49ers undoubtedly was passing on both Patrick Mahomes and Deshaun Watson in 2017. And while hindsight is 20/20, San Francisco's coach is willing to admit as much.
"Anybody who had a chance to take Patrick Mahomes or Deshaun who didn't, everyone knows ... yeah, everyone wishes we had a time machine," Shanahan told The Athletic's Tim Kawakami on "The TK Show."
It's an obvious blunder now and there's no telling what the state of the 49ers franchise would be had they selected either Mahomes or Watson with the No. 3 overall pick of the 2017 NFL draft, rather than defensive lineman Solomon Thomas. But context is key, and Shanahan provided some as to why the 49ers made the pick that they did.
"When I came here ... I think we had the 32nd-ranked defense, the 31st-ranked offense, didn't have a quarterback, and that is risky," Shanahan explained. "And you have the second pick in the draft and you look into all the stuff. Now, before I came here, I had a very good idea that we would be able to get a free-agent quarterback the next year, one that I knew you could win with. So you're looking into these rookies, we've got the second pick in the draft, and no one at that time was considering those guys top-five picks, top-10 picks. But people knew that they had some ability."
The free-agent QB that Shanahan referred to most definitely was current Minnesota Vikings quarterback Kirk Cousins. Shanahan served as Cousins' offensive coordinator during their time with the Washington Football Team, and there was no shortage of rumors suggesting mutual interest in a reunion with San Francisco.
The possibility of adding Cousins on the free-agent market, combined with a roster-building assessment, ultimately pushed the 49ers in Thomas' direction.
"When we came here, my goal was always to hopefully build a D-line," Shanahan continued. "I thought the D-line is kind of what gets you to the Super Bowl, but you've gotta have the quarterback to do it, so which one is going to come first? And you have guys that weren't being classified as top-10 picks yet because no one thought they were exactly a slam dunk yet, and so do you want to make that risk now? Or you know you have something next year, so why don't you just look at other positions and try to build this team, because our team isn't totally ready exactly for a quarterback right now?"
Thomas never lived up to the billing of the third overall pick, totaling just 6.0 sacks across 48 games (30 starts) with San Francisco. The 49ers declined his fifth-year player option and moved on from him last offseason. Meanwhile, Mahomes and Watson have established themselves as two of the best quarterbacks in the game, with the former having beaten the 49ers in Super Bowl LIV.
Obviously, knowing what he does now, Shanahan would have gone about things differently in 2017. But he insisted that their regret resulting from passing on Mahomes and Watson did not compel the 49ers to select Trey Lance this past April.
"That was just a different time," Shanahan added. "There was a different situation, and hell yeah I wish I could go back and have Patrick Mahomes or Deshaun, and I think every other coach on the planet feels the same. But this is two separate cases, and I don't compare Trey to those guys, either. I just know how important that position is. I know where our team's at."
Shanahan and the 49ers have thrown all their chips in the Lance basket. If he becomes the player they believe he can be, it won't erase their biggest draft mistake, but it could overwrite it.