Great article by Maiocco:
With improvement in some areas and decline in others, this team is no better than last year's and may, in fact, be a little bit worse.
It's hard to tell if Smith has progressed or regressed. After looking sharp against GB, DET, NYJ, and BUF; his recent performances against NYG and SEA indicate that the confidence and poise that were cornerstones of his turnaround under Harbaugh are waning. He seems to be forcing things (perhaps to keep Kaepernick on the bench) and panicking in the pocket like he had done so often before 2011. The passing game should have been vastly improved with a second year under Harbaugh and co. and a revamped WR corps. Yet it continues to sputter and be inconsistent. Smith's performance in Arizona will certainly be worth monitoring, as it may answer a few questions and foreshadow what's to come down the road.
The run game has definitely improved, but as a whole, this offensive unit can not seem to capitalize on opportunities and gain/build on leads when they should. They're lacking the "make-a-play-when-they-need-one" element. But then again, they did much of this last season, letting teams hang around for far too long despite physically dominating them.
On the defensive side of the ball, the secondary's play/coverage has improved a considerable amount, which has helped make SF the number one passing D in the league. Conversely, the pass rush and rush defense have regressed. The rush D is still pretty good (holding opponents to under 100 yards a game) but the pass rush is really struggling to put QB's on the ground. Opposing QBs are flushing out of the pocket and making plays when coverage can no longer hold up. With the expected and understandable decrease in turnover ratio, the 49ers were going to have to make up for it with a formidable pass rush and better secondary play. So far, only one of those has come to fruition. And while a solid secondary is great, a fierce pass rush is more valuable as it can help mask deficiencies in the secondary.
Lastly, special teams, as Matt noted, have taken a significant dive--mainly in terms of coverage. I'm sure there are other contributing factors, but this team is really missing Blake Costanzo.
Your thoughts, as well as thoughts on my response, are greatly appreciated.