Undefeated 49ers still have room for improvement

SANTA CLARA - Halfway through the season, the 49ers still haven't lost. But some of the lasting images from their latest win were negative. Of course, images aren't everything. The 49ers beat the Cardinals, played hard and are the only undefeated team in the NFL. Still, as the coaches and players would admit, some things are concerning.

Richard Sherman missed a tackle near the sideline, and Arizona Cardinals wide receiver Andy Isabella ran 88 yards for a touchdown in the fourth quarter. Call that lasting image No. 1. Five 49ers defenders streaked down the field, all with chances to bring down Isabella, and none did. They looked like a slapstick act, not an elite defense, as they chased in vain.

Sherman stormed to the sideline, sat on the bench and screamed at defensive backs coach Joe Woods as Woods listened and nodded. Lasting image No. 2.

After the game, Sherman leaned across a podium with his eyes wide open, eagerly awaiting critical questions. Still seething. Lasting image No. 3.

“That was a humbling game,” he admitted. “We need to be humbled on all levels. Everybody will watch the tape and judge themselves critically, because we can't play like that. That's not championship football.”

Sherman sounded like the 49ers had lost.

Of course, they didn't lose. They won 28-25. But they were challenged by a team that probably will win no more than six games this season. Here are five concerns the 49ers must address.

1. The secondary.

It still hasn't faced an upper-echelon quarterback. The best one the 49ers have faced this season is Arizona's Kyler Murray, who posted a 130.7 passer rating against them.

The secondary should improve when cornerback Ahkello Witherspoon returns from a foot sprain and a quad strain. He was by far the 49ers' best defensive back before he went down Week 3. But it's not clear when he will return.

“It's day to day at this point,” Witherspoon said Thursday in the locker room. “Definitely close to being 100%, but no timetable.”

The 49ers originally expected Witherspoon to return by now.

“He had a setback about 10 days ago,” head coach Kyle Shanahan explained.

While Witherspoon recovers from his setback, the 49ers' starting corners are Emmanuel Moseley, who gave up the 88-yard catch to Isabella last Thursday, and Sherman, who, at the age of 31, has lost speed.

“There's nobody who understands the game at his position better than he does,” Seattle Seahawks coach Pete Carroll said of Sherman on a conference call. Carroll coached Sherman the first seven years of Sherman's career. “He's savvy, smart, tough, he's a playmaker.”

Sherman certainly makes plays - he has intercepted three passes this season. But he also has given up 14 first downs. No one else on the 49ers has given up more than five.

Sherman has a surgically repaired Achilles tendon, is not as quick as he used to be, and struggles changing directions, So, he plays far off opposing receivers to prevent the long catch. As a result, he gives up lots of shorter catches.

The 49ers need Witherspoon back ASAP.

2. The run defense.

The past four games, the 49ers' defense has given up a gargantuan 5.5 yards per carry. That's not championship football, as Sherman would say. The 49ers must improve their run defense, or it could hold them back in the playoffs.

“It's little things,” linebacker Fred Warner said, “little assignment miscues, guys not wrapping up here and there. Things we can fix.”

Warner doesn't sound concerned about the run defense, and neither does Nick Bosa. “You don't want to make excuses,” Bosa said, “but it's all things we can fix. We will get them fixed.”

The 49ers' run defense issues certainly seem fixable, but the fixes might come from the coaches instead of the players. The past two seasons, the 49ers' run defense ranked seventh best out of 32 teams. It was a strength of the 49ers.

This season, the 49ers changed their defensive scheme to super-charge their pass rush at the expense of their run defense. They adopted a “Wide 9” alignment, which puts huge gaps between the four down linemen, gaps opposing teams have begun to exploit in the run game.

Now, the 49ers' run defense ranks 22nd. They might consider using the Wide 9 less frequently and going back to their old scheme when appropriate.

3. The weak-side linebacker position.

The strength of the 49ers' defense is their talented, deep defensive line. Duh.

But the leader of the defense is Kwon Alexander. Or, was Alexander. He tore his left pectoral muscle last Thursday against the Cardinals and will miss the rest of the season.

“Since Day 1, the defense has been what it is because of him,” middle Warner said of Alexander. “He was playing at a Pro Bowl level, but the things people didn't notice is what really made him stand apart.”

Things like what?

“Overall confidence,” Warner said.

Meaning Alexander made the 49ers' defense feel elite. Now he's gone, and his replacement is a rookie fifth-round pick - Dre Greenlaw. Greenlaw can't replace Alexander's leadership, or his elite coverage. Alexander allowed a quarterback rating of just 19.8 this season when targeted.

But Greenlaw potentially can improve the run defense. Alexander missed seven tackles this season. Greenlaw hasn't missed one yet.

“He's a special young talent,” Dee Ford said of Greenlaw. “His play will speak for itself. He will jump off the screen.”

4. The health of George Kittle.

He is the 49ers' best offensive player, the guy they can least afford to lose. Their best blocker and their best receiver. And they might not have him Monday night against the Seahawks.

Kittle suffered multiple injuries against the Cardinals and didn't finish that game. Then, he had an MRI. “There were issues,” Shanahan explained. “He has things in his knee and ankle. Hoping he can play this week, but we'll see.”

It sounds like Kittle won't miss many games, if any, but his injuries could linger throughout the season. Meaning he may not be 100% healthy, and the 49ers might not have full Kittle for a while. They might have only partial Kittle.

Learning to win without their best offensive weapon could help the 49ers, but they need him fully healthy when the playoffs start.

5. The passing game when the opposing defense blitzes.

Jimmy Garoppolo has some good numbers. His quarterback rating is an impressive 100.6, and his completion percentage is an even more impressive 70.8.

“To complete over 70% of your passes is really a challenge,” Carroll said. “Garoppolo has a real quick release, good athleticism to move around the pocket and find space, and seems to be a really good complement (to the 49ers' running game).”

Here's what Carroll didn't mention: Against the blitz, Garoppolo's quarterback rating is just 63.6, he has thrown four touchdown passes and five interceptions and his quarterback rating is a meager 77.8.

Maybe Garoppolo doesn't quite trust his pass protection - both starting offensive tackles have missed significant time. Or maybe Garoppolo doesn't quite trust his surgically repaired knee after tearing his ACL last season. Maybe he gets apprehensive when the other team blitzes.

Whatever the reason, Garoppolo needs to find a solution, because teams will blitz him heavily until he finds one.