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Why the 49ers won’t look at Colin Kaepernick

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We’ve been down this road before, let’s go down it again.

The San Francisco 49ers worked out a number of quarterbacks in wake of the Jimmy Garoppolo season-ending knee injury. For now, C.J. Beathard will be in the driver’s seat for 2018 barring absolute disaster, but Nick Mullens is behind him, and anyone who can man the backup job may be an improvement.

One of the more notable names not on the list of invites was Colin Kaepernick. Of course this brought back the questions (and debates) that this was part of some of the more wider issues keeping him out of the league. So the 49ers are part of this madness with the league colluding and it’s an anti-Kap stance right?

Not so fast.

His skillset is not a fit in Kyle Shanahan’s offense

Go back and watch the tape of Jimmy Garoppolo. Watch how he stays in the pocket, sometimes where it’s not to his benefit. Shanahan’s offense is predicated on pocket passing and accuracy. Two things when said together Kaepernick has never been able to do well with consistency. Has Kaepernick had good games staying in the pocket? Yes, but more often than not, Kaepernick’s accuracy suffered when he was contained in the pocket. Kaepernick’s threat is a a couple reads and then taking off which gashed defenses. The roll outs he did were absolute killers as well. I don’t think there’s a better quarterback who throws (or threw) rolling out. This made him a great fit for Seattle’s offense, or whatever they ran a year ago.

Kaepernick is also a huge threat with the read option. He has the uncanny ability to fool everyone in the stadium (including the person operating the camera) on if he handed it off or kept it. Shanahan has respect for the read option and thinks it’s a valuable part of any NFL offense, but he doesn’t rely on it near as much as Kaepernick may need it. That’s a valuable skill that just won’t be taken advantage of if he runs Shanahan’s offense.

Creating an offense to highlight Kaepernick’s skills stunts the growth of the rest of the offense

When Kaepernick took over for Alex Smith in 2012, the 49ers’ playbook transformed. No longer were they relying on short/intermediate throws and a power run game, instead they implemented the pistol formation—something Kaepernick was comfortable with from his college days in Nevada. From the pistol, the 49ers then went to other more traditional formations, but the read option was Kaepernick’s bread and butter and they outright embarrassed the Green Bay Packers by running it. There were two reasons for this: the built offense was something to help Kaepernick be comfortable as he transitioned into more of a pocket passer and got more familiar with the NFL level (which resulted in the opposite effect), and it was also seen at the time as the evolution of the NFL game.

Before becoming the starter, Kaepernick ran the ‘Kaepernick package’ exclusively, which was where the 49ers pulled Smith for a down and used Kaepernick’s legs. The 49ers thought long-term and knew that Kaepernick was the answer, as was running the read option into other formations, so they changed the offense on the fly to have this package the focal point. It was used less in later years, but the plays used instead required little diagnosing of defensive coverages (a known weakness, and something crucial with the current offense). Since it takes longer than a year for someone to get acclimated as a QB at the NFL level, it may have made the decision easier since Kaepernick would be running this offense for longer than 13 games.

Kaepernick is not the future in San Francisco anymore. To take advantage of what he brings to the table would require re-tooling Shanahan’s offense for 13 games — which means everyone will be going to the Kaepernick offense. That’s all fine and good, except the team is very young and in a developmental season. Shanahan wants consistency in his offense. He doesn’t want them playing an offense to be discarded at season’s end. He wants reps in the Jimmy Garoppolo, pocket passing, traditional west coast offense. And those second year players are getting further immersed in the intricacies of it. Remember, this is one of the harder offenses in the league, but once mastered it’s devastating—just ask the Atlanta Falcons. Putting Kaepernick in there means those reps turn into something else and for the age of this team, reps in the offense they will be running for years to come is far more important than reps just to win. It’s putting the players in a position to succeed long-term. Shanahan’s offense is hard enough to learn as it is, might as well focus on that than change everything. The 49ers are not in win-now mode, nor do they have a quarterback of the future they want to get playing time or evaluate. Changing everything hurts the future of what they have around the quarterback—and who would be sticking around at season’s end.

And if they decided to run Shanahan’s offense—no adjustments, just what are they going to run with Kaepernick coming in without a training camp? So now everyone is held back as they play a stripped down playbook with what they can teach Kaepernick in a short amount of time, which, again stunts the growth of a team developing in a specific mold.

If Kaepernick did not opt out, he would have been cut

When John Lynch and Kyle Shanahan took over, they had a sit-down with Kaepernick. The two were very transparent about their plans and Shanahan’s desire to run an offense similar to the one he ran in Atlanta. It led to Kaepernick opting out of his contract, but had he not done so, he would have been cut according to reports.

So what does the past have to do with anything? Well, if you were given an ultimatum to resign from your job or be fired—and you had an option to return two years later, would you be jumping up and down?

I doubt it.

Despite the fact that Trent Baalke is gone, as are a lot of the front office members who gave Kaepernick all the headaches post-Harbaugh, Paraag Marathe remains—and he has fingerprints on that team-friendly deal Kaepernick got in the first place. While there has been no documented beef between the two, it’s been reported Marathe was never much of a Kaepernick fan.

Now, it’s probably a given Marathe isn’t whispering in anyone’s ears to keep Kaepernick out but given all the history between the 49ers and Kaepernick, would that make sense to bring him back after all of that? And there may be others in the front office as well.

No, this has nothing to do with his protesting

The 49ers are not denying Kaepernick because of his protesting. Could he be a distraction? Given his history, status with the fanbase, and Beathard’s uninspiring rookie campaign, it’s possible, but it’s so there’s not a divide in the locker room over him starting or something along those lines, if you want to take it there. The fact he could kneel during the Anthem has nothing to do with that distraction.

Remember, the 49ers were nothing but supportive of Kaepernick’s protest then and now. 49ers owner Jed York publicly said he abstained from voting against any Anthem regulations choosing instead to hear more from his players. York also mocked the whole thing in a way by closing down concessions when the Anthem plays. The 49ers have also matched Kaepernick’s many contributions to organizations fighting inequality.

Point is, of the 32 teams in the NFL using “football reasons” as an excuse to not sign Kaepernick due to some larger issue, the 49ers are one where that statement could potentially be sincere.