In my opinion, talent and system are needed for success. A prime example is the Patriots, to me anyway. They don't always have the best talent year in and year out, but it's their system. Take the year Brady was out and Cassell stepped in, they still had pretty good success. Throw Brady in to that, who is immensely talented at his position, and that team takes on another level.
Now take the Eagles. That first year Chip came in, talent level was crazy. Eagles took the league by storm with their high octane offense and relied heavily on the talents of Jackson and McCoy, and don't forget the talent on both the offensive and defensive lines. All that has been changed and look, they're just not the same team. Same system, just alot less talent.
As for Kap, his confidence is at an all time low. I hate to say it, but you can tell he doesn't have that "swagger" that he usually does. His flaws are becoming more and more obvious as each game progresses and that's because the system they have in SF right now, is not a good one. It's not fitting to the talents of their QB or the talents of their other positions for that matter. Throw in the fact you have a new head coach who has never even made the ranks of a coordinator, it's a recipe for disaster.