Colts vs. 49ers: Takeaways from San Francisco's 27-7 Loss to Indianapolis

Dylan DeSimone@@DeSimone80Correspondent ISeptember 23, 2013

Colts vs. 49ers: Takeaways from San Francisco's 27-7 Loss to Indianapolis

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    Cary Edmondson-USA TODAY Sports

    The reigning conference champion San Francisco 49ers are in a state of emergency following the Week 3 27-7 loss to the Indianapolis Colts.

    All sorts of things that would’ve seemed unfathomable under coach Jim Harbaugh’s watch have been coming to fruition, leaving San Francisco’s season hanging in the balance before it truly even had a chance to begin.

    Prior to Sunday’s game, quarterback Colin Kaepernick was a perfect 5-0 on his home turf at Candlestick Park, while the 49ers team had remained undefeated following losses under Harbaugh (7-0). Both streaks were snapped like a wishbone after a Thanksgiving feast.

    Even worse? The aftermath.

    This game—and all of the burning storylines going into it—came with several inherent implications. Following an uncharacteristic loss and slipshod start to the season, this game would predominantly gauge where the 49ers stood in what was hopefully going to be another run to the Super Bowl.

    Of course, following the loss, the immediate future of this team quickly spiraled down a dark tunnel that may lead to nowhere in 2013. This is a team as a whole that looks like it needs to regroup and go back to the drawing board. 

    After a surprise 1-2 start to the regular season, here is what we learned about the San Francisco 49ers.

    This is the 1st time the 49ers have had a losing record with Jim Harbaugh as their head coach

    — ESPN Stats & Info (@ESPNStatsInfo) September 22, 2013

Public Enemy No. 1: Greg Roman

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    Kyle Terada-USA TODAY Sports

    Fans and analysts can continue to blame Kaepernick and his struggles on offense. As the quarterback, a lot of the blame should fall on his shoulders. However, we’ve seen what No. 7 can do. It is on the coaches to get that out of him by putting him in a position to succeed, and they have failed to do that.

    The primary reason, and it was first noticed in Week 1, was the abandonment of the ground attack.

    San Francisco became one-dimensional all of a sudden, putting it on Kap to throw on first, second and third down. Even though the Niners were facing the No. 29 rush defense in the Colts, and did not have Vernon Davis (hamstring) active, they continued to call passing play after passing play.

    On Monday, if not before then, there will be a lot of fingers pointing at offensive coordinator Greg Roman, who functions as the play-caller. So far in 2013, there has been little to no emphasis on the run. Roman and the offensive staff appeared to be so enamored with Kap that they felt it was okay to put more plays in his hands and sit back and wait for results.

    It is lazy play-calling, and it has drastically veered from what San Francisco’s true identity is, which is power rushing and play action.

    Just 10 points in last 7 quarters for the 49ers. Where is Greg Roman?

    — Matt Miller (@nfldraftscout) September 22, 2013

49ers Defense Has Lost Its Swagger

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    No more stopping the run. Fewer pressures. Even less sacks.

    The 49ers defense has completely fallen off a cliff here, allowing an average of 28 points per game in three weeks played. This once-feared front seven allowed 235 rushing yards and three rushing touchdowns in the first two weeks and did not fare much better on Sunday versus Indianapolis.

    Both Trent Richardson and Ahmad Bradshaw went off, each finding the end zone and combining for well over 100 yards between them. Bradshaw, the veteran free-agent running back, had the bulk of the yardage on the ground, nearly breaking the century mark himself (95 yards).

    Andrew Luck even had a rushing touchdown off a bootleg, bringing the total to three scores on the day.

    This has been hurting the 49ers because it was always a big part of their strategy to make an offense one-dimensional. With their All-Pro linebackers and clogging D-line, they would clamp down tight and restrict what offenses could do. Eventually, an opposing offensive coordinator would abandon the run, and repeatedly throw, playing right into San Francisco’s hands.

    It seems on Sunday, the 49ers were given a taste of their own medicine.

    If this defense cannot find itself, the 49ers are going to have a tough time bouncing back from this two-game losing streak.

What Is Going on with the Offensive Line?

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    It is a bit of a surprise, seeing as how it was a strength last season, but the 49ers offensive line has not played up to par the past couple of games.

    Sure, it has had to adjust to Kaepernick’s unorthodox style, which includes leaving the pocket fairly often. All things considered, it is probably much easier to protect a statue of a quarterback since offensive linemen don’t exactly have eyes in the back of their heads. But the pressure has been getting to Kap regardless.

    He has been under fire, which has drastically affected his passer rating, especially when the Niners aren’t utilizing play action.

    While this line is strong from left to right, it's been asked to pass protect way more than it'd ideally have to. The Niners have several maulers on this O-line, including three first-round picks and two bona fide Pro Bowlers, so the mere fact that they have not taken advantage and run behind this crew is arguably the most perplexing thing.

    That overall loss of identity has caused this offensive line group to get in a funk and not play to its true potential.

    When the players are pumped up and feeling good from bowling over defenders and moving the ball on the ground, they have a little extra fire in pass protection.

    Juiced from all that adrenaline, they get geared up to knock guys down, and that’s when you really see them finish their blocks. Again, the coaches need to fix this funk on offense so one of their most prized assets, the O-line, can get back into a rhythm and allow this unit as a whole to operate in all facets.

    As bad as the 49ers passing game was this week, the biggest concern from past two games is how the line have been whipped.

    — Pete Prisco (@PriscoCBS) September 23, 2013

Injuries Are Killing the 49ers Slowly

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    Kelley L Cox-USA TODAY Sports

    Serious Injuries

    Michael Crabtree, WR (Achilles)

    Mario Manningham, WR (ACL)

    Ian Williams, DT (Ankle)

    Chris Culliver, CB (ACL)

    Critical Dings

    Vernon Davis, TE (Hamstring)

    Patrick Willis, LB (Hand, Groin)

    LaMichael James, RB (Knee)

    It is evident that the injury bug has bitten the 49ers. It seems like every week, the injuries continue to mount, as the team just can’t stay healthy. Apart from the majors that were made clear prior to the season, the 49ers lost nose tackle Ian Williams for the season in the Week 2 loss to the Seahawks.

    LaMichael James—a weapon the 49ers were counting on to contribute—has yet to be active for a regular-season game in 2013, having sprained his MCL in the third week of exhibition play. His inability to contribute has hurt a San Francisco team that is starving for playmakers.

    All-Pro linebacker Patrick Willis and Pro Bowl tight end Vernon Davis, the team captains, have not been able to stay healthy either. Willis broke his hand in the offseason and left Week 3 with a groin pull, which is always difficult to gauge in terms of a timetable for return.

    Meanwhile, Davis pulled his hamstring against the Seahawks and was not active in the team’s second consecutive loss.

    Altogether (plus a lack of their rookie class), the 49ers do not look like they’ll be able to endure all of these injuries. The most painful of which appear to be the losses of Michael Crabtree and Chris Culliver, who were the respective stars of the receiving corps and the defensive backfield.

    @49ers Patrick Willis has a groin injury and is OUT for the rest of the game. #INDvsSF

    — Michelle Beisner (@MichelleBeisner) September 22, 2013

It’s Going to Get Worse on Defense…

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    Cary Edmondson-USA TODAY Sports

    Shortly after the Week 3 loss to Indianapolis, it was confirmed by 49ers team president and CEO Jed York that linebacker Aldon Smith would be taking an indefinite leave of absence to seek treatment for alcohol and drug abuse, via Michelle Beisner of NFL Network.

    Smith was involved in an off-the-field incident in the early hours of Thursday morning, which resulted in his arrest. After crashing his car into a tree and blowing a .15 BAC for San Jose police, the All-Pro defender was booked into county jail before being released on a $5,200 bail.

    Despite exhaustive media scrutiny, the 49ers linebacker started and played close to 100 percent of the defensive snaps on Sunday.

    The Niners appeared to handle this situation delicately, not rushing into sending Smith to a facility until he was committed to getting better. He is an asset they’ve invested in and want to see to it that he improves his quality of life. However, effective immediately, the 49ers will have to prepare for life without No. 99. 

    @49ers Aldon Smith, "I want to apologize. I will work to get it fixed."

    — Michelle Beisner (@MichelleBeisner) September 22, 2013

Penalties, Penalties and More Penalties

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    The 49ers have completely gotten away from the fundamental football that Jim Harbaugh and Co. first instilled in 2011.

    When all else failed, it was their bread and butter, and it kept the team in virtually every game. By playing a cleaner brand of football, which included winning the turnover battle and not committing penalties, the 49ers gave themselves an edge. It is safe to say, the 49ers have lost that edge.

    Three weeks in, and San Francisco is still one of the most penalized teams in the National Football League.

    The cornerbacks have been drawing pass interference and holding calls like hot cakes, while the O-line has been called for false starts. Not to mention the fact that San Fran has had to prematurely use its timeouts to avoid delay of game penalties at times. Foolish penalties like unnecessary roughness and unsportsmanlike conduct flags have also been prevalent this season.

    This is been a significant part of the team’s drift away from its identity under Harbaugh.

    That's 5 defensive penalties on the 49ers today. Wow.

    — Eric Edholm (@Eric_Edholm) September 22, 2013

Road to the Playoffs?

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    Cary Edmondson-USA TODAY Sports

    With only three weeks in the books, some might say it is a little premature to already talk about the postseason. But in the NFC West, where every single game counts, it is never too soon to project where the 49ers might be.

    All things considered, San Francisco does not look like the class of the division right now.

    While they are the reigning division and conference champions, the 49ers appear to be playing second fiddle to the Seahawks, who look to be firmly in charge with a two-game lead to start 2013. They have played better with the injuries they’ve endured, and the game-planning from one year to the next has not changed as drastically as San Francisco’s has.

    Moreover, the 49ers are already 0-1 against the NFC West, riding a two-game losing streak and are going on the road on a short week to play the St. Louis Rams, which have not lost to the Niners since 2012.

    Each year, San Francisco’s No. 1 goal is to win the division. It is not off to a very good start.

    That awkward moment when the Jaguars scored 14 more points against the Seahawks than the 49ers did.

    — Faux John Madden (@FauxJohnMadden) September 22, 2013

49ers Need a No. 2 Wide Receiver

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    As we mentioned before, the 49ers are hurting without Michael Crabtree in the lineup. Originally, the perception was that the 49ers would be able to supplement No. 15’s production in the aggregate, fielding an attack by committee.

    Kyle Williams and Quinton Patton have been the top two options behind Anquan Boldin, but neither has sufficed so far.

    Williams only has nine grabs for 87 yards and no touchdowns to start the 2013 season, while the rookie Patton has yet to record his first career catch. This is disconcerting for the 49ers, which have failed to establish a run game and have a young signal-caller with no security blanket.

    The lack of balance in the passing attack has been an issue since Week 1, even in their win over the Green Bay Packers.

    Over time—and not much at that—the 49ers have become exploitable. The fact that no one has emerged in Crabtree’s absence has allowed defenses to clamp down on Boldin, who functions better as a complementary weapon. If they fail to get a second wideout going, it might not matter by the time Crabtree and Mario Manningham return.