Kaepernick’s brilliance masks issues for 49ers

Here is my Monday column. Enjoy.

SANTA CLARA – Let’s focus on the good after the 49ers’ Week 1 win over the Packers, a very good team, probably not a great team.

THE GOOD

After just 11 starts, Colin Kaepernick probably is the best quarterback in the NFL. You could say he singlehandedly beat the Packers. His defense gave up 28 points, he had no rushing attack and still he put on one of the best passing performances in franchise history. He made Anquan Boldin look like Jerry Rice.

Kaepernick made up for 11 penalties, eight missed tackles and Jim Harbaugh’s time-consuming play-calling system which puts Kaepernick and the 49ers’ offense up against the clock on almost every play. Kaepernick’s sheer brilliance masks almost every area of concern on the 49ers’ roster.

Perhaps “area of concern” is too strong. With Kaepernick, the 49ers are one of the best teams in the league. But he has to mask a few things that could prevent the 49ers from winning the Super Bowl this season.

Now, let’s monitor what Kaepernick is masking. You can bet the 49ers and their opponents are monitoring these things as well.

THE RUNNING GAME

The 49ers didn’t have one on Sunday. The Packers made sure Kaepernick didn’t run, and then they stuffed Frank Gore like a teddy bear, holding him to 44 yards on 21 carries.

Harbaugh didn’t seem concerned about his rushing attack at his Monday morning press conference. “They were playing it to stop the run,” he said, “and then we passed.”

Fair enough, but this isn’t a one-game slump for Gore. Over the past 13 games, he’s averaged 3.8 yards per carry, below average for an NFL running back and almost a full yard per carry worse than his career average of 4.6. He’s 30 years old, so it’s tough to imagine Gore reversing this trend.

On Sunday, he couldn’t run out of the I-formation, the Pistol or the Shotgun. And neither could his backup, Kendall Hunter. He had one carry when he ran through a hole the size of a crater and picked up 23 yards, but other than that he gained just one yard on five carries.

THE SECONDARY RECEIVERS

Against the Packers, Anquan Boldin and Vernon Davis caught 70 percent of Kaepernick’s completions. That needs to change. Kaepernick can’t consistently beat teams with his arm if he’s passing to just two receivers.

Tom Brady won Super Bowls passing to less talented receivers than the 49ers’ current group, but he spread the ball around. He didn’t throw it to one or two guys over and over again.

You can bet the Seahawks will try to force Kaepernick to pass the ball to Kyle Williams or Vance McDonald or Marlon Moore or any of his unproven receivers.

THE PASS RUSH

Two seasons ago, the 49ers had arguably the best pass rush in the NFL. Justin Smith was an MVP candidate that year. But last season, even before he injured his elbow, he had become almost a non-factor as a pass rusher recording just three sacks. And as a result, the 49ers’ pass rush was just so-so.

Against the Packers, Justin Smith never touched Aaron Rodgers, and neither did Ahmad Brooks. The only pass rusher who played well was Aldon Smith, and he was facing a rookie fourth-round pick at left tackle.

The 49ers wanted to improve their pass-rushing depth this offseason, so they spent a second and third-round pick on the position taking Tank Carradine in the second and Corey Lemonier in the third. Carradine is injured and may not play this season. Lemonier is healthy, but he played only special teams on Sunday.

The 49ers need more pass-rushing production from Brooks in particular. It may be unrealistic to expect Justin Smith to be more than a run-stopper at this stage of his career.

THE CORNERBACKS

This group is the 49ers’ biggest weakness. In the past they’ve been masked by the pass rush and the explosive offense. They were double-masked. Against the Packers, the 49ers’ top-three corners – Carlos Rogers, Tarell Brown and Nnamdi Asomugha – got exposed.

According to Pro Football Focus, Asomugha gave up a 105.3 passer rating, Brown gave up a 118.8 rating and Rogers gave up an abysmal 158.3 rating.

Those numbers are particularly alarming when you consider the 49ers knew the Packers were passing practically every play. The Packers abandoned their running game in the first quarter yet the 49ers’ corners still could not cover the Packers’ receivers.

DEFENSE IN GENERAL

Sunday’s game was a perfect representation of what the 49ers’ defense has become. They gave up 28 points and 385 net yards to the Packers’ offense. Over the 49ers’ past seven games, they’ve given up 27.4 points per game and 387 net yards per game. So, the 49ers’ defense didn’t underperform on Sunday. It played like it normally plays.

If those averages had been the 49ers’ averages for the entire 2012 regular season, they would have ranked 30th in points allowed and 31st in yards allowed.

Defense used to be the most important part of the 49ers. Now, it’s what Kaepernick must mask and overcome.

This is not an alarm call. The Niners are very good. But they have issues. As long as Kaepernick continues to lead the offense to more than 28 points per game, consider the issues masked.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for the Press Democrat’s website. You can reach him at grantcohn@gmail.com

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