The San Francisco 49ers were my preseason choice to win the Super Bowl. After their opening win against the Packers, I felt like a genius. Their offense was all but flawless, and they looked like the dominant team they were expected to be. But then they played at Seattle. Then hosted Indianapolis. In both games they were incompetent on both sides of the ball. It was ugly. Really, really ugly. Now we are left to pick up the pieces.

Is this team still a serious contender that has just hit a rough spot early in the year? Or are they a flawed squad that will wind up falling well short of expectations? Let’s take a look:

Colin Kaepernick

You can’t talk about the team without starting with the QB. Against Green Bay he was a weapon. Since then, however, he has been a liability. His passing has been inaccurate, and against Indianapolis he was a non-factor on his feet as well. There are a number of factors that could be contributing to these issues. For starters, aside from Anquan Boldin, this team has issues with targets for Kaepernick — especially last game when Vernon Davis was injured. As significantly, it’s important to remember that Kaepernick is far from an experienced starter. He only took over halfway through last year. He has not faced real adversity, so he is understandably struggling to deal with it. I’ve read all sorts of theories in the last two weeks — that his style of play has been decoded by opposing teams being the recurring theme. I don’t buy it. Peyton Manning was brutal at the start of last season, but he can still play football. Tom Brady has been mostly lousy so far this year, but no one is writing him off. If this trend of poor play were to continue for several more weeks, then there could be an issue. Until then, though, it’s far too early to panic.

Smith drama

Off-field drama can be a real problem for a team — especially when it happens close to game time. Aldon Smith has struggled for a while now, according to reports, and that came to a head with his DUI incident last week. He played last week when he probably shouldn’t have and has since left the team to attend rehab. Smith is young, but he is already perhaps the most important figure in a very good defense. That his struggles have impacted the team should be far from a surprise.

Run defense

Last year, opposing teams didn’t score their first rushing touchdown against the Niners until Week 15. They have already allowed six rushing touchdowns. That’s really all you need to know about the issues in this area. The question, then, is if this is just a short-term issue or a symptom of larger problems. The cast of characters in the front seven is basically the same as last year, so the issues shouldn’t be lasting. With Smith gone for a while and Patrick Willis potentially out with a groin injury, though, there may not be immediate improvement on this front. If they can’t stop the run, they could be in trouble.

Secondary

If you can’t stop the run, you had better be able to stop the pass. Unfortunately, they have struggled here as well. Corner Chris Culliver tore his ACL in camp, so their best CB is gone for the year. Nnamdi Asomugha was a good gamble, but it certainly hasn’t paid off. Safety Dashon Goldson has been missed now that he is a Buccaneer. The good news is that teams have thrown less on the Niners than any other team in the league. The problem, though, is that when they do throw they are reasonably successful. This is far less of a concern than it appears, though. If the front seven tightens up, that will benefit the secondary. So will time — with new personnel, including rookie safety Eric Reid, time and experience together will build chemistry and increase success. They have the talent to be solid.

Depth of issues

While none of the issues we have discussed by themselves appear to be fatal, the concern is the number of them. If one of those issues was clearly the problem, then you could rely on what has gone well to build on. The problem, though, is that nothing has gone well for this team recently. They have been just plain bad. That can change, but they are running out of time. A record of 1-2 can be overcome, but with Seattle looking legitimate and having a win against San Francisco already in their pocket, there isn’t a lot of room for error.

Schedule

The team faces a short week this week with a Thursday night date in St. Louis. That could be a bad thing, but I actually like it — it gives the team less time to feel sorry for itself. After that they have two home games, two reasonably manageable road games — one a gift in Jacksonville — and then a bye week. By that Week 9 bye they absolutely need to be at least 4-4, and ideally better than that. The schedule sets up reasonably well for that possibility — even without dramatic improvements in all of the problem areas. At least there is some good news here.

Public expectations

The last bit of good news here is that the public has been quick to jump off this bandwagon. The team was the 6/1 co-favorite to win the Super Bowl at Bovada before the season began. They have already fallen to 12/1. It is easier for the public to lose faith than to have it restored, so there will be value here in the short term if the team does show progress against their demons.

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