It's amazing that people just assume all this is the fault of scheme.
Kaepernick's first TD: Clay completely jumps up the field, vacating his gap, and Neal spins inside, taking him out of his gap as well. Kaepernick just runs through it and scored.
Another play in the 2nd Q, Capers brings the blitz. Clay, again, vacates his gap by trying to get around the RB/FB through going around him. Kaepernick runs through the hole that creates and gets a first down.
Kaepernick's longest TD run in the game: Walden has set the edge and, instead of holding it decides to bite and moves towards the RB on the play-action. Kaepernick has an open lane to run through.
If you think any of that was planned by Capers, then you are absolutely an idiot.
The problem isn't the scheme. The game plan from last week would have worked. That said, Capers should have adjusted and had a spy on Kaepernick. He has some questions to answer, no doubt.
Beyond any single thing, though, we need play makers. Outside of Clay, there is no other playmaker on this team. Woodson isn't any more. Hayward has much to learn. Raji has his moments, but cannot be counted on for 60+ plays game in game out. Nick Collins is gone. Bishop is out injured.
We still need talent. More playmaking talent, to be precise. Changing some position coaches may be in the cards, but nothing will substitute for the fact that we never had the talent to match-up with a talented 49ers team. Add to that: 14 49ers points off 2 Packers' turnovers gave us a hole that was near impossible to climb out off.
The NFL: Where Greg Jennings Happens.