#5: Discipline and Penalties
It's been pretty disturbing how many penalties we've had early in the season. Offensively, it feels like we're not playing fundamentally well. The Rams game was an encouraging sign because they seem to be improving. On defense, we have a lot of Unnecessary Roughness calls for illegal hits, justified or not (Donte Hitner). And overall, extracurricular activity after the whistle. It's incredibly annoying because it feels like our guys are just defending or retaliating to cheap shots from opposing players (Example: Clay Matthews and the Packers). Our team definitely has taken some of Coach Harbaugh's hot-headedness. Even though it's not always their fault, it's always the second guy who gets flagged.
#4: Greg Roman's Playcalling at Pivotal Moments
I think everyone knows what I'm talking about when I say "4th and 6." Many people weren't fans of Roman's playcalling in the Super Bowl, and that's honestly been the one blemish in his career as the 49ers' OC. He has the most brilliant moments at times, but then other times, we wonder what he's thinking.
#3: Late Season/Playoff Defense
Despite giving up a lot of yardage and points early on this season, the unit still looks great. Their problems have been more about the offense's deficiencies. The Rams game was more about what they're all about. Despite that, it all depends on how the coaching staff manages our defense late in the season. One of the bigger criticisms of last season was that our veterans played too much and were understandably gassed by the late season and playoffs. It feels like the coaching staff is resting our guys more, but the defense's performance late in the season will be important.
#2: Wide Receiver Situation
If we didn't have Anquan Boldin, we'd be in a lot of trouble. A.J. Jenkins didn't pan out, while Crabtree, Manningham, and now Patton are all injured. I have no doubt in my mind that when Manningham and Crabtree return, our offense will explode, but the question is... how many games will our receiving corps cost us until they're here? We're 2 games behind the Seahawks (IMO the #1 obstacle to the Super Bowl) and the WR situation is going to be important in the middle of the season. I've been unimpressed with what Kyle Williams and Marlon Moore have been able to do. But with Jon Baldwin getting traded to us and learning the offense, I think he's our one hope in being that #2 guy to Boldin, until Crabtree and Manningham get here.
#1: Seattle Seahawks (and Denver Broncos)
The beginning of this season's Seattle game offered some hope, because we had some opportunities. There's a chance to win there if we have Crabtree & Boldin, a third WR steps up (between Manningham and Baldwin), VD & Frank Gore do what they always do, and the defense plays stingy... In other words, our team has to be complete and we have to be perfect. But during the playoffs, I just don't know how it's going to go. Quite honestly, I don't know if we can win in Seattle.
We have to hope that we can catch up to them over the course of the regular season and eventually beat Seattle in our home game to clinch the division. And then if we beat the Seahawks and make it to the Super Bowl, there's still the Broncos, who have looked invincible this season.