I would say injuries would be the primary big one, followed by bad calls in close games.
We really were only 1 game away from not locking up HFA even after our incredible start, and SF's average start...they still caught us.
I think the Cards have improved while the Niners have improved, but only slightly. The Cards are aging along the DL, but are still damned good there. The Washington suspension hurts them, but they make up for it on the backend I think. Strangely enough, their secondary might be the strong point of that team, and I still think the way we beat them is through the air with our new weapons and Harvin.
I theorize that the Niners will lose some production from aging positions, but improved with Stevie Johnson. The caveat here is can Kaepernick take advantage of having a very good 4th option ? I honesty haven't seen it yet, but that is the crux of the Niners upcoming season right there: can Kaepernick improve ? If he can't, they probably split with the Cards. If he can, we might be in trouble. The Bowman injury hurts them; they have quality depth but it's not Bowman's caliber (what is?) so they drop off there.
Their secondary is an unknown. They've shored up the backend with Bethea, but he's not a great Safety against the run. I think J. Smith is due for a decline. Aldon Smith will likely lose some time due to suspension, if the Niners are unlucky (so far they dodged a huge bullet legally) he'll see 8 games. If we can win that game down there, it is HUGE for us winning the division; it's the only game I have us losing for certain this year in division.
STL is really all about whether Bradford can get that offense together. If he can, they're going to challenge for the division. Their secondary is still weak, but that front 7 is shaping up to be one of the best in the NFL.