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Kaepernick should’ve been starting before Week 6

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SANTA CLARA — Colin Kaepernick still has accuracy issues and he’s not the 49ers’s quarterback of the future.

But it’s hard to deny San Francisco has looked better on offense the last two weeks. And Kaepernick has pretty much everything to do with the upgrade.

Despite dropped passes and no running game, Kaepernick was carrying the 49ers against Arizona and tied the game up with a throwback 57-yard touchdown drive. The week prior against New Orleans, he tossed 398 yards, two touchdowns and one regretful interception. Kap has turned Quinton Patton into a more productive player (4 catches, 55.7 yards per game in the last four weeks). And he’s averaging 57 rushing yards per game, the same amount Todd Gurley has averaged this season.

The evidence is coming to the surface: Kaepernick looks like a much more serviceable player in 2016 with Chip Kelly than he did last year under Jim Tomsulsa.

Which means Kaepernick should’ve been starting before Week 6. It’s another decision this 49ers regime got wrong.

The team will say Kaepernick simply wasn’t ready to play Week 1. There was a three week period where Kelly insisted Kaepernick’s playing weight wasn’t up to starting standards  — something the quarterback politely refuted from his locker room pulpit. The 49ers were also at fault for giving him arm fatigue in August, where he missed two preseason games and had to battle rust when he returned. A respected surgeon told us any NFL player coming off three offseason surgeries should not be working a full load during training camp.

We can read between the lines: Kaepernick finally got back onto the field when his agent and GM Trent Baalke sat down at the negotiating table. The contract renegotiation should’ve happened much sooner. The 49ers put cap room in 2017 ahead of winning football games in 2016. They actually convinced themselves Kaepernick was not better than Blaine Gabbert.

In what could’ve been a season changing moment in Week 4 against the Dallas Cowboys, Gabbert missed a wide open Torrey Smith. The play should have been a triumphant 55-yard touchdown and the 49ers would be riding a 2-2 record into a Thursday Night Football matchup with Arizona. Instead, the season spiraled out of control after that moment.

Hindsight is 20/20. And maybe you think Kaepernick is barely an upgrade over Gabbert — after all, the 49ers are still 0-4 with Kap at QB. But there’s certainly no talk of benching Kaepernick. And this defense is much more responsible for losses, at least against Buffalo, Tampa Bay and New Orleans.

In protect his job mode at the podium on Tuesday, offensive coordinator wasn’t ready to admit the offense has been better under No. 7’s direction.

“No, I wouldn’t say that specifically,” said Modkins. “I think our offense is growing. I think our offense in general is learning more and more about what we’re asking from them and where they need to be in all those type of situations. I wouldn’t say it’s specifically because of Kap. I think our guys grew a little bit last week. Probably couldn’t say that the week before.

“There’s no doubt he’s doing some good things. He’s been improving. Let’s look for that to continue. He has a long way to go, just like me. Just like all those other guys on offense.”

How much better would the 49ers’s record have been if Kaepernick started the season under center in Week 1? Probably not by much. Some of you will argue it’s much better for this team to be 1-8 than 3-6. The 49ers need a superstar player for the future and the best chance to land one is to lose as many games as possible.

But with better coaching and a couple of roster tweaks, Kelly and Baalke legitimately thought this team could improve upon its 5-11 record from 2015. If not, they would have added free agent acquisitions. The 49ers did not come into this season expecting to tank. Job security for general managers and coaches in the NFL is too precious to mess around with.

Things in Santa Clara could’ve been different in 2016 had Kaepernick begun the season as the starter.

Whoever stood on the table for Gabbert to start, and to continue starting well into the season, deserves some internal scorn for flawed decision making.