What a difference a week makes, huh? This time last week the 49'ers and their QB couldn't be stopped. This time last week there were articles that read, "Chip Kelly's offense takes NFL by storm".
Whenever something new-fangle comes into the NFL, you can always bet the best way to stop it, is go back to the basics. Stop the run and make these QB's become pocket passers and you will take them out of their eliminate. Although Colin Kaepernick has a solid above average arm, there is a lot more to be an above average passer than just having an above average arm. Like being able to read defenses under pressure.
The basics---gap responsibility and outside containment. 8-9 in the box and force these guys to throw the ball. If they spread out, dont spread out. Stay in your core base defense. They spread you out to create running lanes. Dont give them that. Take away what is between the tackles and force these teams to throw the ball 30 plus times a game.
But you also need to be able to run the ball on offense. These teams are trying to wear down defense by running 70-100 plays a game. There is only one solution for that. Pound the football and eat up clock. And that too is from the basics of football.