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We knew Colin Kaepernick's days were numbered, but 49ers should have handled this better

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The San Francisco 49ers have benched quarterback Colin Kaepernick, replacing him with Blaine Gabbert. The move is not surprising as the leak process began in earnest a couple weeks back. The team could have handled this better.

The San Francisco 49ers are now 2-6 going into their Week 9 contest with the Atlanta Falcons, before their Week 10 bye. Yesterday, we received the news Vernon Davis was to be traded to the Denver Broncos in exchange for a swap of its sixth and seventh round picks in 2016, and the 49ers get the Broncos 6th round pick in 2017. That was quickly followed by Kyle McLorg's report that Colin Kaepernick was going to be benched this week, and replaced by Blaine Gabbert.

Last week, Niners Nation brought forward a source from Jim Harbaugh's coaching staff, who shed some light on Colin Kaepernick. The coaching staff wholeheartedly believed Kap would get better after the Super Bowl. And, they worked with Kaepernick, his reads and his pocket presence. Kaepernick showed improvement in all areas, except one.

Over the past couple years, Kaepernick has made some spectacular throws, which made many believe he had the ability to get it right. The former coaching staff said they would see a certain look from their opponent and make the call to allow Kap to air it out, but something did not click. Think back to the wins in 2013-2014, when Kap was asked by reporters what he liked about a certain receiver, as an example, Anquan Boldin or Michael Crabtree, he always would state, "he gets open."

In retrospect, Kaepernick's comments are really telling. Critics everywhere talked about Kaepernick's inability to read defenses or lack of touch, among other things. But, after watching Kaepernick play against the St.Louis Rams, a few more things came to mind.

The source seemed to hone on one thing, that is, Kaepernick's inability to trust his receivers to be open by the time the ball got there. If he did not see his receiver open, he would move on too quickly or stare down the receiver trying to get open.

In many football situations, and especially with an inferior offensive line, a quarterback has to get the ball out and to a very specific location, trusting that his receiver will be there as called. And, our source said, "there were so many times, we thought ‘this is it' and Kap would let it go. But, he didn't."

On the other hand, on NFL Network, the 49ers owner stated his revamped coaching staff will do a better job of putting players in a "position to make plays."

York used that variation of the "position to make plays" phrase on five occasions. And he suggested the 49ers would use the dual-threat quarterback Colin Kaepernick to make more plays with his feet in 2015.

"You've got a great guy in (quarterbacks coach) Steve Logan that's coming in that's going to work with him on fundamentals and allow us to put together a system that's going to put Kap in the best position to make plays," York said. "How many quarterbacks in this league can run 90 yards for a touchdown? I can't think of many.

"But you've got to put Kap in a position where he can make those plays. And put Kap in a position where we can run the ball. We can throw the ball in ways that allow him to be successful, and let him be the absolute stud that he can be on the field. And I think that's what you're going to see from us next year. Defenses are not going to want to play against us because you're not going to know where we're going to hit you."

According to our source, Kaepernick would wait too long to get rid of it and scramble. Alternatively, by the time he saw the receiver getting open, he would try to power the ball like a rocket. By attempting to get the ball there as fast as possible, there was no touch on it and led to several drops.

In the Arizona game, the last time we really saw Kaepernick throw the ball, it led to many interceptions. Again, by the time he saw an open receiver, so did the defense and he was picked.

Last year, the offensive schemes made little sense to fans, but in my opinion they were experimenting with different play action in an effort to let Kap get confident and trust the wide outs to make the play. And, this theory is supported by the comments of the 49ers wide receivers.

Anquan Boldin made it a point before the game in New York to give Colin Kaepernick a few words of encouragement.

"I didn't want him to put pressure on himself," Boldin said. "I told him to just put it on us. Let us make the plays for you. Just take the pressure off yourself and go out and have fun and let it rip."

Tracy Sandler interviewed Vernon Davis this last June and this is what he had to say on  Colin Kaepernick:

"I feel like we're definitely in a rhythm. And I feel like we're getting somewhere as far as trust. And it's all about trust. That's what football is about. Kaepernick has to trust that I'm going to be where I have to be... Now he has to believe in that, because he should be able to throw the ball off his back foot...with one eye open, because he knows that I'm going to be there. And that's what it's about. You have to have that. But I feel like we're getting somewhere. I feel like we're on the right track. We're on the right path. We're definitely trying to keep it all together."

While Vernon Davis has endured a lot of heat for his calling out Kaepernick in a team meeting, it is my impression he was really trying to help Kap understand the vantage point of a receiver. And, apparently, whether it was his approach or his attitude, he never got through to Colin Kaepernick. And, apparently neither did Boldin.

In light of my story last week, I wanted to put some of my thoughts down on this subject. I have asked Jed York personally for an interview, but have been largely ignored. Given the fact he stays away from local media, I am not delusional enough to think he would pay me any mind. Nonetheless, it would not surprise me if the media leaks and articles relating to Colin Kaepernick being "on an island" is simply more of the same from the front office.

Another source stated the person who leaks the information is not Jed York, but Paraag Marathe. Apparently, Marathe was the main person responsible for the leaks regarding Jim Harbaugh last year and it seems likely he is partially responsible for the Kaepernick drama. Even if York did not leak the information himself, his office seemingly is involved in it. At the very least, York and the other execs cannot keep their feelings discreet. Or, the execs purposefully use it as a tool to gain public support of their decisions.

Over a year ago, I heard first hand someone tell Jed York the rumors surrounding Harbaugh seemed ridiculous because Harbaugh was such a great coach. York quipped that a "great" coach would have won that Super Bowl. According to Niners Nation's latest source, Jed York would openly state he believed Tomsula could win more games than Harbaugh. That had to be a major division between Harbaugh and Tomsula.

Another source indicated to me some time ago, Marathe was never quite on board with Kaepernick due to his perceived "professionalism". And, from the very beginning of Kap's career, the national media ferociously criticized his urban clothes, backwards hat, headphones and et cetera during press conferences. But, those criticisms did not really connect with the San Francisco fan base. In fact, many (including this site) defended his dress. Yet, it still bothered Marathe.

Just as the 49ers execs were willing to deal with the idiosyncrasies of Harbaugh when he won, the 49ers execs did not push Kaepernick to change so long as he won games. However, now that the team has fallen to 2-6, Kaepernick is wearing a suit and tie and it is not difficult to see the same pattern of the front office exercising its power for Kap to conform to its standards of professionalism.

The San Francisco 49ers have transparency, but it is not the kind they would like to have. We saw what happened with Jim Harbaugh last year, and it appears to be happening again to a similar extent with Colin Kaepernick. From the beginning of this "reload" situation, the frustrating part is the 49ers' inability to come out and explain to the fans the problem and outline a clear direction. Unfortunately, they point fingers, and use scapegoats and drama to announce decisions. The 49ers execs owed it to Kaepernick and to fans to come forward and announce that Kap was being benched and why. We'll see when it actually happens.