49ers flaws were exposed and the rest of the league was watching

Here is my Tuesday column on the issues the 49ers currently face.

The Week 1 win against the Packers masked issues on the 49ers, but the Seahawks just tore off the mask. What do we see?

The offense is worse than it was last season. Let’s start there.

They’re missing key players: Michael Crabtree, Mario Manningham, Delanie Walker and Frank Gore. Yes, Gore is missing. More on him later.

Crabtree and Manningham may or may not come back. They’re recovering from serious injuries and we don’t know if they can be effective this season.

Delanie Walker, a key receiver and blocker the past two seasons, is not coming back. He’s a Titan. The 49ers replaced him with a rookie, second-round pick Vance McDonald who is not a good blocker yet and has caught just two passes in two games.

And then there is Gore. He may never come back even though he’s still a 49er.

His legs are gone. They no longer have the snap or explosion or whatever you want to call the thing a running back’s legs need.

Maybe he’s still tired from the playoffs. As you get older, it takes longer for your legs to come back. Maybe he’s trying to compensate in the weight room by doing more explosive exercises and only further fatiguing himself and ending up with dead legs. Whatever it may be, he doesn’t seem to be able to explode through tight holes or bounce runs outside this season.

Bad combo.

He averaged 2.6 yards after contact per carry the past two seasons according to Pro Football Focus. He’s averaging just 1.5 yards after contact per carry through two games this season. He may or may not be able to get his legs going periodically, but definitely not consistently.

To get the running game going, Jim Harbaugh and Greg Roman need to get clever. The pistol isn’t working. Gore keeps getting hit in the backfield. Runs from the pistol don’t hit the line of scrimmage as quickly as runs from under center.

In 2011 and 2012, the 49ers’ offensive line dominated defenses on trap plays and power off-tackle runs. Old-school plays. The 49ers hardly have run any of those plays this season. That needs to change right now.

And the 49ers need more production from their passing game, too. That may be difficult.

They have just two proven receiving threats – Anquan Boldin and Vernon Davis – and Davis pulled his hamstring against the Seahawks. If the 49ers have to play the Colts game without him – and they may, hamstring pulls typically take a few weeks to rehab – the offense could be bad.

The Colts’ defense could load up against the run, double-cover Boldin and force Colin Kaepernick to throw to Kyle Williams or Vance McDonald or Quinton Patton or any of the other 49ers’ receivers NFL defenses aren’t scared of. That’s a no-brainer game plan most NFL defenses can execute.

Then there’s the 49ers’ defense. It has issues of its own, particularly stopping the run without a nose tackle on the field.

The 49ers use their Nickel defense when the opposing offense puts three receivers on the field. Out of necessity the 49ers spread out their defense leaving big holes for the running back. On those plays, the 49ers’ have a front six, not a front seven, and their front six gets gashed in the running game.

Week 1, the 49ers’ nickel defense gave up 5.2 yards per carry and a touchdown to Eddie Lacy in the second half. Week 2, The Seahawks’ backup running back Robert Turbin averaged 5 yards per carry, and starter Marshawn Lynch averaged 5.9 yards per carry and scored a touchdown against the Niners’ Nickel D. Those are terrible numbers for the 49ers.

Opposing offensive coordinators know those numbers. Expect teams to pound the ball out of three and four-wide-receiver formations against the 49ers’ defense until it shows it can stop those runs.

The 49ers used to be the best run defense in the NFL. Two seasons ago, they didn’t give up a rushing touchdown until Week 16. They’ve already given up three rushing TDs this season. See a pattern here?

The past two seasons, the 49ers’ strengths were running the ball on offense and stopping the run on defense. Until further notice, those areas are weaknesses.

What else do we see when we take off the mask?

The 49ers have committed 23 penalties for 206 yards through two games, second-worst in the league in both categories. Last season, they committed 121 penalties for 960 yards. They’re almost doubling their pace from last year and last year’s pace was one of the worst in the NFL. Bad.

There’s been so much hype about this team. Some experts already have declared them Super Bowl winners. But their issues could be serious, a deal breaker. When you take off the mask, you don’t see a young, virile, handsome stud. You see a tired, aging warrior who can’t get out of his own way.

The 49ers are in need of immediate cosmetic surgery, the facelift to beat all facelifts.

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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