Colin Kaepernick struggling to keep pace with adjusting defenses

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It was a year ago right now that Colin Kaepernick exploded on to the scene as a starting quarterback in the NFL, making the game look almost easy with his blend of dynamic playmaking and dual-threat athleticism. The San Francisco 49ers started him ahead of veteran Alex Smith for the first time in Week 11 of 2012, and rode Kaepernick's strong right arm and knack for devastating defenses with his legs in the read-option offense all the way to a Super Bowl berth in New Orleans.

But the game hasn't looked easy for Kaepernick for most of 2013, and his season has been a complicated one. Other than a fantastic Week 1 showing in a defeat of visiting Green Bay, when he threw for 412 yards and three touchdowns, Kaepernick's statistics at best have been downright ordinary this season, and at 6-3, the defending NFC champion 49ers face an uphill climb to win their third consecutive division title and lay claim to one of the conference's top two seeds and a coveted first-round playoff bye.

In Sunday's 10-9 loss to ascending Carolina in Candlestick Park, Kaepernick endured his worst game as a pro, taking a career-high six sacks, completing just half of his 22 pass attempts for a career-low 91 yards, with one interception and an anemic 42.0 passer rating. The 49ers offense generated just 151 yards and 10 first downs, converting just 2-of-13 third-down situations (15 percent), with a 17-yard Frank Gore gallop representing the team's longest gain.

Those were the worst offensive numbers of the three-year Jim Harbaugh coaching era in San Francisco, and it was the third time already this season the 49ers have been held to fewer than 10 points in a game, which never happened last year once Kaepernick took over the No. 1 job.

After the egg-laying against the Panthers, which snapped a five-game 49ers winning streak and might have sentenced San Francisco to the No. 6 seed in the NFC playoffs, Kaepernick's struggles understandably took the spotlight. This did not look like the same trend-setting player who was on the cover of every magazine this preseason and was supposed to lead the 49ers back to the Super Bowl, where they would finish the climb to NFL supremacy. This looked like a young quarterback whose game has hit something of a wall and is in need of mid-course correction, with defenses having adjusted to his skillset this season better than he has adjusted his plan of attack.

ESPN analyst and former 49ers quarterback Trent Dilfer created a bit of a buzz Sunday night, saying on the air that Kaepernick this season has not fared as well because defenses have taken away his first read, rendering him a "remedial'' passer who has not learned how to comfortably work through the rest of his receiving progressions.

Reached Tuesday, Dilfer said while Kaepernick remains "an incredible player and an incredible athlete,'' his development as a passer has "plateaued'' this season, and he hasn't made enough progress in his second season as a starter.

"I would be concerned if I were the 49ers, because there hasn't been a lot of improvement on his part as a passer,'' Dilfer said. "He can threaten more than as just a traditional passer, but you still have to develop as a passer. And he's kind of stayed to this point as a passer who takes his first read and sticks with it. But if they take your first read away, that's pretty much it. You don't work deep through your progressions, you don't get the ball out to other receivers.''

Clearly Kaepernick has not posed the same threat as he did last season, when he completed 62.4 percent of his passes, threw 10 touchdowns and just three interceptions in the regular season, with a sterling 98.3 rating. Even when he runs the ball, which he only did four times for 16 yards against the Panthers, he's doesn't resemble the game-breaker who bedeviled defenses on the ground in 2012, with 415 yards on 63 carries, five touchdowns and a 6.6-yard average carry.

Clearly, part of the problem in Kaepernick's second season as a starter -- maybe the biggest part -- has been the 49ers' receiving depth chart. It might shock you to learn that San Francisco's passing game ranks dead last in the NFL, averaging just 173.9 yards per game, and that's not even close to the team in the No. 31 slot (Bay Area rival Oakland, 187.6). Kaepernick has thrown just nine touchdown passes against six interceptions this season, and that split is a pedestrian six-six in his past eight games. He has four games this season with a completion percentage of 50 percent or less (he had none in 2012), has thrown for more than 200 yards and completed as many as 16 passes only once since Week 1 and his passer rating has slipped to a mediocre 83.1.

That's why I've come around to the notion that no injury in the NFL was more consequential this year than the Achilles' tear suffered by 49ers No. 1 receiver Michael Crabtree in a May OTA session. Robbed of his favorite target and the team's lead pass-catcher from 2012 (85 catches, 1,105 yards, nine touchdowns), Kaepernick has not adjusted well.

When you factor in that the 49ers' second-leading receiver from last year, Mario Manningham, made his season debut Sunday against Carolina after being out since his Week 16 ACL injury last December, and tight end Vernon Davis has missed parts of three games this season (all three were San Francisco losses), the blame for the 49ers' passing game issues should be spread around liberally. Even the loss of tight end Delanie Walker in free agency and Randy Moss to retirement have seemingly hurt Kaepernick's game, removing targets with which he was familiar.

The trade for veteran receiver Anquan Boldin looked like a godsend in the opening-week win over Green Bay, when his monster game of 13 catches for 208 yards and a touchdown saved the day. But since then, Boldin has produced just 28 receptions for 366 yards and one more touchdown in the ensuing eight games, and his lack of vertical speed has shown up, particularly when Davis has been forced out of the lineup due to injury.

"I think that's part of what we've seen this season,'' Dilfer said. "That's definitely part of the problem, because any time you lose integral parts of your passing game, it's going to affect it. But it's not as if the guys they still have are chopped liver. Because I still think this is the best roster in football. So even if it's just baby steps, and getting just two percent better every week, you want to see the quarterback continue to progress.''

The hope in San Francisco is that the worst is over in terms of the passing game's struggles. Manningham is back, Crabtree last week was cleared to start practicing and could be activated any day now, and though Davis left last week's loss with a concussion in the second quarter, it's not thought to be a long-term injury.

But that may be glass-half-full thinking. Manning is coming off ACL surgery, and it typically takes a while for the player to regain his previous burst, and that same reality awaits Crabtree, whenever he is activated and resumes his No. 1 receiver role. Better health aside, there do not appear to be any miracle cures on the horizon in San Francisco, and the 49ers' season more likely will rise or fall from here on the strength of their superb defense and how much Kaepernick and the team's coaching staff figure out some solutions to what is limiting the passing game.

Kaepernick has to do a better, more patient job of finding his receivers, even if his first option isn't there or he's forced to throw a few guys open, a skill he has yet to show much feel. And his receivers need to start helping him out more, getting better separation and consistently winning their share of jump balls.

Harbaugh and offensive coordinator Greg Roman need to do their part, whether that means going back to more of the read-option attack that Kaepernick thrived in last season, which limits how much he has to read, or calling a game that prioritizes his legs and keeps the chains moving with plenty of shorter, underneath passes, rather than the downfield patterns that San Francisco has found so ineffective.

Kaepernick is at that point in his development where it's up to him and his coaches to account for the adjustments that defenses have made to him. The quarterback who picked apart the Packers in Week 1 and made all those magazine cover stories look justified still exists. And a low playoff seed does not rule out a long postseason run, as we have often learned in recent years. But the 49ers' passing game needs to get healthier and reinvent itself to some degree between now and the start of the playoffs, and it would be great if that process got underway during San Francisco's challenging trip to NFC South-leading New Orleans (7-2) this week.

It was in the Superdome last November, in a 31-21 49ers win in Week 12, that we started to get a real feel for the width and breadth of Kaepernick's playmaking talents. His stellar play that day vindicated Harbaugh's decision to bench Smith and ride with his young, second-year quarterback. Now, as Smith and 9-0 Kansas City Chiefs prepare to play the game of the year in the NFL at 8-1 Denver, the juxtaposition of Kaepernick facing another big game in New Orleans (site of last year's Super Bowl) is somewhat inescapable. But if he plays well and the 49ers win, it'll do a lot to calm the escalating fears in San Francisco that this season will be one of regression.

More likely, as he approaches just his 20th career start, Kaepernick's current problems are growing pains that must be endured and worked through. The results have not been the same, but the talent is still there. He has not made the game look quite so easy this season, but there's still time to figure out the complications of what defenses are doing to him and his team, and make something far beyond ordinary out of 2013.