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Pete and Wes look ahead to Sunday's game between the Packers and the Colin Kaepernick-led 49ers. (Sept. 30, 2015) Weston Hodkiewicz and Pete Dougherty | Press-Gazette Media

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Seems like the question du juor in the NFL is, “What’s wrong with Colin Kaepernick?”

You’ll have to forgive the Green Bay Packers and their followers if they’re even more perplexed than most about the decline of the San Francisco 49ers quarterback, who is coming off a 47-7 loss to Arizona in which he threw two pick-sixes and four interceptions total.

The Packers on Sunday will face Kaepernick for the first time in about 21 months, and it’s difficult to square the Kaepernick they've lost to with the one coming into this game.

This is the same player who looked like a Hall of Famer in three straight wins over the Packers, including two in playoff games, from January 2013 through January 2014. Yet now the 27-year-old who led the 49ers to the Super Bowl three seasons ago and is entering his prime is the most embattled quarterback in the NFL. His passer rating has dropped from 91.6 in ’13, to 86.4 in ’14, to 71.1 three games into this season. His won-loss record has dipped from 12-4 to 8-8 to 1-2 so far this season. And he's the talk of the league because of his brutal performance at Arizona.

For educated opinions on what's happened, we turned this week to two NFL scouts who have studied Kaepernick the last few years as rivals of the 49ers in the NFC West Division.

The scouts were aware of the prevailing recent criticisms of Kaepernick, including that he doesn’t read defenses well and that he has shaky throwing mechanics and poor touch. Neither had those high on their list of issues.

In fact, one dismissed them as possible deal breakers for Kaepernick’s chances to succeed.

“Yeah, he was in a spread offense (in college at Nevada), but he still had to know where to go with the ball,” the scout said. “He can stick it on a receiver, he can throw to areas where the defender is not. He can do the back-shoulder fades. The ball does tend to get away from him just a little bit.”

Both scouts also were in agreement that Kaepernick has the talent to be a winning quarterback in the NFL because of his remarkable athleticism and strong, though sometimes erratic, throwing arm. But only one was bullish on Kaepernick actually doing it.

“There’s nothing wrong with Kaepernick other than them trying to make him throw from the pocket,” the scout said.

The other scout likewise sees a player whose talent worries defensive coordinators. But he questioned whether Kaepernick has the temperament to succeed long term.

The scout contrasted Kaepernick with another young quarterback in the NFC West, Seattle’s Russell Wilson.

Kaepernick has more physical talent – their 40-yard dashes are about the same, in the low to mid 4.5-seconds, and he’s a much bigger man at 6-feet-4 5/8 and 230 pounds to Wilson’s 5-10 5/8 and 206. Kaepernick also has a higher score on the Wonderlic intelligence test – 37 points, which is third-highest among starting quarterbacks in the NFL, to Wilson’s 28.

Yet, none of those measures the leadership and willpower that helped Wilson get to the last two Super Bowls and win one of them.

“I don’t think Kaepernick has those kind of skills,” the scout said. “Leadership is about sustaining a belief. The smartest guy in the room is looked at as the smartest guy in the room, he’s not (necessarily) looked at as a leader.”

When asked about the root cause of Kaepernick’s problems, both scouts included two team issues: The 49ers’ decline on defense and on the offensive line over the past year. That’s combined to put more of the offense on Kaepernick.

Both scouts agree with another of the prevailing theories of Kaepernick’s struggles: that former coach Jim Harbaugh tried to make him too much of a pocket passer last year.

The numbers say Harbaugh didn’t change Kaepernick much last year – according to Pro Football Focus, about the same percentage of his passes were straight drop-backs last season as in 2013. But in both scouts’ study of game tape they saw a coach who'd changed the emphasis of his offense to protect his quarterback from hits even if raw numbers suggested otherwise.

In fact, one of the scouts called it the primary reason Kaepernick has regressed. The scout said he understood Harbaugh’s thinking but thinks the coach was trying to make Kaepernick into something he’s not.

“He knows how to get out of bounds,” the scout said, “he knows how to slide, he hasn’t been hurt. I’d just trust in him that he’ll stay healthy. A lot of his production comes outside the pocket. When they tried to make him strictly a pocket passer, that’s when they messed his mind up.”

What might jump out to Packers observers is that Kaepernick has beaten them as a runner and from the pocket.

In the divisional round of the playoffs in the 2012 season, the game in which the 49ers brought out the read-option in full force, he ran for 191 yards in the 49ers’ 45-31 win. That’s the NFL record for rushing yards by a quarterback in a playoff game.

The Packers devoted a good part of that next offseason to defending the read option and took it away from Kaepernick in the 2013 opener by playing their run-stopping personnel – that is, their 3-4 base defense – most of the game. But that came at a price in pass coverage, and in the 49ers’ 34-28 win Kaepernick shredded them for 412 yards passing, which remains his career high, and a 129.4 rating.

In the teams’ third meeting, the wild-card round of the playoffs at the end of the 2013 season, the Packers kept Kaepernick mostly under control. He passed for only 227 yards and a 76.3 rating on the night and going into the fourth quarter had put up only 13 points. But with the game on the line, Kaepernick came through with two go-ahead drives – one for a touchdown and one for the game-winning field goal as time expired.

It’s probably no coincidence that on those two drives, Kaepernick had two scrambles for 35 yards.

“He only needs to pop off two or three (runs),” said the scout who’s bullish on Kaepernick. “He doesn’t need any 80-yard runs, just first-down runs, get you into the red zone runs, that type of stuff, to make that offense effective.”

The other scout pointed to the 49ers’ front-office dysfunction last year as the bigger catalyst for Kaepernick’s slide.

The split between Harbaugh on one side and general manager Trent Baalke and owner Jed York on the other reportedly goes back to short, failed talks for a Harbaugh contract extension in 2013. The relationship further deteriorated after York and Baalke entertained the possibility of trading Harbaugh to the Cleveland Browns in February 2014, and by early last season the fissure between the abrasive coach and his two bosses became a soap opera that lasted until the sides parted shortly after the regular-season finale.

“People say the players don’t care about that,” the scout said. “Yeah, they do, and it affects them. A couple guys came out in defense of Harbaugh, then a couple came out and said he’s too demanding and wears everybody down. When you have that kind of stuff going on, you’re going to struggle.”

The bullish scout thinks that at 1-2 and coming off the horrendous game at Arizona, 49ers coach Jim Tomsula and offensive coordinator Geep Chryst will emphasize the dual-threat aspect of their offense this week against the Packers. That would mean running halfback Carlos Hyde extensively and mixing in Kaepernick on occasional read-option runs, bootlegs, quarterback sweeps, roll outs, waggles (moving pockets) and quarterback draws.

“He’s a sandlot guy, just like Russell Wilson,” the scout said. “When he’s outside the pocket and he starts slinging the ball or he has an option to run, that’s when D-coordinators go, ‘Wow.’ They’re laughing (right now), going ‘Yeah, keep him in the pocket so we can come get him.’ If (the 49ers) decide to let him loose a little bit, you’ll see a much different quarterback.”

— pdougher@pressgazettemedia.com and follow him on Twitter @PeteDougherty.

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