My thoughts on the problems on this team:
Number One issue is offensive coaching. They mentioned last week that Alex Smith had 180 plays on his wristband (or was it 185?). There is no way a team can get proficient on 180 plays. I think they need to have something closer to 60 plays, and become experts at running those. Unfortunately, this can't be solved until the training camp next year. KC also demonstrated how to effectively run against a team that is trying to stop the run. It wasn't running up the middle. I am not sure if Frank Gore could execute those runs, but Brian Westbrook certainly could.
Defensively, the 49ers are not playing well. I suspect that Haralson and Lewis are the main problems, but I am not sure their replacements are currently on the team. Reggie Smith can take Lewis place, but I don't know that we have a good replacement for Haralson. It also seems that the defense cannot adjust to what the offense is doing, which is a coaching issue.
Alex Smith is playing decent, but I suspect that he won't want to return to the 49ers next year. He is better off going to another team, and learning their offense than learning a new offense with the 49ers. He is playing well enough, that I suspect that he will make decent money in the free agent market.