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Bill Barnwell on What Went Wrong with the 2014 49ers: Why Kap shouldn't shoulder the blame, and why axing Harbaugh would be a bad decision.

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Bill Barnwell:

It was ironic that Sunday began with rumors that Harbaugh’s predecessor, Mike Singletary, was likely to be offered a head-coaching job somewhere in 2015. You have to look back at Singletary to remember just how low this franchise once was. Under the stewardship of Dennis Erickson, Mike Nolan, and Singletary, the 49ers went 46-82 over an eight-year stretch, often failing to meet modest expectations while struggling to develop a quarterback. Alex Smith was nearly out of football by the time Singletary, whose public doubting of Smith once inspired the crowd in San Francisco to chant “We Want [David] Carr,” was fired late in the 2010 season.

Harbaugh took over with Smith as his quarterback and immediately turned things around. Even including this disappointing 7-6 season, the 49ers have gone 43-17-1 under Harbaugh, leaving them with the fourth-best record in football over that time frame. They narrowly lost one Super Bowl and came within three turnovers of making it to two more, with Kyle Williams fumbling away one NFC Championship Game with a pair of mishandled punts in 2011 and Colin Kaepernick’s three-minute drive ending with a Richard Sherman–influenced pick in 2013.

It’s Kaepernick, of course, who has joined Harbaugh as the target of San Francisco criticism this season. On one hand, it’s a reasonable complaint. Kaepernick, who I once believed could have an MVP-caliber season if things broke right for him, is actually having his worst season as a starter, with his QBR falling from 72.2 during his breakout 2012 half-season and 68.6 a year ago to just 52.2 this season. He looks unsteady and uncertain under center, always a step too early to run and a step too late to recognize his open receiver and get the ball out. The almost preternatural accuracy he exhibited during that 2012 campaign has slowly disappeared, making his throws more difficult to bring in.

More than anything, Kaepernick is turning the ball over more frequently. Sunday was no exception, as he threw an interception on the very first play from scrimmage to a team that had been forcing takeaways on a league-low 5.2 percent of drives. Kaepernick would also throw a pick to Charles Woodson in the fourth quarter to seal the game, ending up with 10 interceptions and seven fumbles in 13 starts this year. That’s already more than his combined 14 interceptions and fumbles from last season.

It’s more than Kaepernick, though. Watch that interception again.Kaepernick initially has time to throw, and while he stares in one direction, there’s more than one receiver in the area. Nobody looks open.2 He doesn’t scramble because he gets happy feet; Kaepernick scrambles because Frank Gore’s cut block attempt on Justin Tuck is fended off, allowing Tuck to easily elude the veteran running back and chase Kaepernick after a slight delay. Kaepernick tries to improvise and has Michael Crabtree head upfield past former teammate Tarell Brown, but Crabtree can’t create much separation, and when Kaepernick doesn’t see safety Brandian Ross, what looks like a sailed pass becomes a pick.

All of that is to say that it’s a team problem on the San Francisco offense. The 49ers are a mess in just about every way an offense can be a mess. That starts with the offensive line, a unit that was once the cornerstone of the team. Injuries, primarily to right tackle Anthony Davis (most recently a concussion) and center Daniel Kilgore (broken leg), have forced the Niners to start six offensive line combos this season, and none of them has looked particularly effective.

Swing tackle Jonathan Martin has been physically overpowered on the right side, a problem both during his time in Miami and here in San Francisco. Rookie center Marcus Martin was inconsistent before suffering a knee injury during Sunday’s loss, leaving the Niners to insert undrafted free agent Dillon Farrell, who will likely be at the pivot in their seventh line rotation, set to debut in Seattle next Sunday. Even former Pro Bowl–caliber guard Alex Boone has been disappointing. It wasn’t a surprise when Boone struggled early in the season after returning from his summer holdout, but the expectation was always that Boone would play his way into shape and return to his dominant form as the season went along. That just hasn’t been the case.

In all, Kaepernick is being pressured more frequently. ESPN Stats & Information notes that the San Francisco offensive line is controlling the line of scrimmage on just 48.5 percent of pass plays, the 23rd-best rate in football. The 49ers ranked in the top 12 in that statistic in both 2012 and 2013. Teams have realized they don’t need to blitz the 49ers to bother Kaepernick. When defenses do blitz, Kaepernick’s QBR is 69.4, which is 11th-best in football. When they don’t send pressure and drop into coverage, Kaepernick’s 55.5 QBR is 26th-best, behind the likes of Josh McCown and Derek Carr. Oakland sacked Kaepernick five times on just 40 dropbacks and made eight tackles for loss.

You might think the blocking woes would have led the 49ers to utilize Vernon Davis’s skills as a pass protector far more often than past years, but they’ve actually used him as a receiver more frequently to try to give Kaepernick an easier target. Davis is running routes on nearly 45 percent of his offensive snaps after settling around 40 percent in 2012 and 2013. It just hasn’t worked. He’s being thrown the ball on only 16.9 percent of his routes, and he’s dropped 8.7 percent of the passes thrown to him, which would rate among the league leaders at tight end if he had enough targets to qualify.

Davis isn’t the only one struggling to get open. While it was natural to hope that Michael Crabtree would be far closer to 100 percent after rushing back from a torn Achilles last season, he has never looked like the guy who posted dominant numbers when Kaepernick first entered the lineup. Crabtree has been slowed by a foot injury, and the mix of subtle acceleration and leaping ability that marked his pre-2013 game hasn’t shown up. Stevie Johnson, who was supposed to give the 49ers one of the league’s best third wideouts after serving as Buffalo’s no. 1 receiver for years, has operated on the fringes of the offense and has yet to become a weapon. He went receptionless on two targets against Oakland.

It’s here where the disastrous 2012 draft is being felt.3 General manager Trent Baalke is rightly regarded as one of the best talent evaluators in football, but he struck out at the top of his 2012 draft in spectacular fashion. The 49ers used their top two picks on skill-position players, neither of whom are still with the team. First-round pick A.J. Jenkins was frozen out of the offense and didn’t catch a pass in his lone season with the 49ers before being traded to the Chiefs for Jonathan Baldwin, who is now out of football. Second-rounder LaMichael James never seemed to regain the trust of the coaching staff after fumbling during the Super Bowl, and he and the team agreed to part ways earlier this season. Relatively high 2013 draft picks like Vance McDonald and the sadly retired Marcus Lattimore have also failed to provide weapons for Kaepernick.

The special teams have also slowly become an eyesore for San Francisco. After posting the league’s second-best unit behind a career year from David Akers and the steady work of Andy Lee in 2011, things have slowly fallen apart. Akers collapsed in 2012. James headed a return unit in 2013 that ranked 25th in combined performance on kicks and returns. And this year, the 49ers have been bad at everything, most notably punts. Poor work on special teams helped tear them apart Sunday, with a holding penalty wiping away one Phil Dawson field goal before the veteran missed a key kick in the fourth quarter. They were even unlucky, with Sebastian Janikowski hitting a 57-yarder that would normally be beyond even his mammoth leg.

Many of San Francisco’s problems have not been obvious; they’ve stretched across places like the offensive line and special teams, where easy narratives fear to tread. Instead, the criticisms have come in for Kaepernick, Harbaugh, and their shared connection. Some have suggested that the read-option is a problem, that people have figured out all the tricks the 49ers have to offer — comparing Kaepernick to the failing dictatorship of Robert Griffin.

That’s just a false construct. The read-option is still doing just fine for teams with better offensive lines and more effective quarterbacks. Hell, you don’t even need that; Blake Bortles was awful virtually all game against the Giants last week and set up the game-winning field goal with two keeps on the zone-read. Russell Wilson and Ryan Tannehill and the Eagles offense are all doing fine. Andy Dalton has run for a pair of read-option touchdowns the past two weeks. Cam Newton looked great yesterday, even at far less than 100 percent. It seems silly to point to Griffin’s obvious physical struggles and try to use that as proof that it’s a tactic on its last legs. Should the NFL stop drafting tall quarterbacks because Zach Mettenberger and Mike Glennon were both bad this year?

Regardless of which tactics they try to use, the problems for the 49ers stem from the team’s lack of execution on offense. I can’t imagine that would get better by moving on from Harbaugh, but the rumor mill refuses to let up. This weekend, Michigan appeared to give up on acquiring Harbaugh, with the suggestion that he wanted to stay in the NFL. Rumors then linked him to the team he was facing, with the Raiders apparently offering Harbaugh the chance to possess the personnel power he doesn’t have in San Francisco. Harbaugh, though, had Richard Sherman and Doug Baldwin at Stanford and didn’t bother to draft either, which could be an indicator of his personnel skills.

In any case, San Francisco’s playoff hopes lie in tatters. Just about everything that could have gone wrong yesterday did. Their division rivals all won, with the Seahawks handling the Eagles, the Cardinals coming up with a narrow victory over the Chiefs, and the Rams delivering an impressive shutout of Washington, making them just the fifth team since the turn of the century to pitch shutouts in consecutive weeks. The 49ers are now 7-6 and down two games on the four 9-4 teams (Detroit, Seattle, Dallas, and Philadelphia) that stand out as likely wild-card rivals.

The 49ers would win a tiebreaker with the Eagles or Cowboys after beating them both, but they’ll need to beat the Seahawks in Seattle on Sunday to stay in the playoff hunt. Some casinos in Vegas have the 49ers as double-digit underdogs for the first time during the Harbaugh era, and given that the Niners have lost by an average of more than 20 points when playing Wilson in Seattle, you can’t really blame them.

If they do lose, the calls for Harbaugh to part ways will just become louder. The compensation will be tricky; my previous estimates suggested Harbaugh could be worth multiple first-rounders, but that was in a different context, before this wildly disappointing season and with more years left on Harbaugh’s contract, which expires after next year. Given all the public chatter, it might be tough for the Niners to get even a first-rounder for their suddenly embattled head coach.

For all that’s happened this year, it would be a shame to see things end. Harbaugh has done an incredible job turning around a moribund 49ers franchise, and his success over the past four seasons is one of the more remarkable runs in recent league history. I don’t doubt the reports that he’s grating. I just doubt that the 49ers can find a better coach. The 2014 49ers were fatally flawed, albeit in more subtle ways than most are suggesting. The 2015 49ers don’t have to be, too.

"In this game, they played the 3rd string center, 2nd string right tackle (who is dreadful), the 2nd TE is the 4th string TE (and the starter has been playing like a 4th string) and no RB. On D, 3rd string nose tackle, 4 and 5th string ILB, and 4th, 5th, and 6th string corner backs. It's amazing how well they're did really."


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