This is what beat the Packers: the run.
Kaepernick shredded Green Bay's defense, which struggled mightily against the read-option and the running threat Kaepernick. Kaepernick ran for the most yards ever by a quarterback. Green Bay has a good defense, but they were simply unprepared.
It's safe to say that the Falcons will be more prepared.
Atlanta upset Seattle on a late field goal after blowing a 20-point lead, as they treated the fans at the Georgia Dome to a game for the ages. And those fans will witness one more game at the Georgia Dome, as Atlanta, who secured home-field advantage, will be hosting the 49ers in the NFC Championship.
The Falcons faced a quarterback similar to Kaepernick in Russell Wilson when they faced the Seahawks in the divisional playoffs, and Wilson shredded Atlanta. He threw two touchdowns, ran for one and almost reached 400 yards, and his only interception was on a last-second Hail Mary.
And it's not just Wilson who has broken onto the scene against Atlanta's weak defense.
As Eric Branch of sfgate.com noted here, running quarterbacks like Cam Newton, Robert Griffin III and Michael Vick have done well against Atlanta, and while RGIII was contained nicely, it doesn't mean that Atlanta hasn't struggled with guys like Kaepernick.
Wilson had lots of time to throw, and he often left the pocket and made plays outside of the pocket. His biggest throw was a short pass to Marshawn Lynch that turned into the play that set up the go-ahead score, and it happened because Wilson had time and was able to scramble out of the pocket and make a play with his feet and his arm.
Should the 49ers Run the Option?
The Seahawks, however, didn't use the read-option much, and Wilson didn't run out of it. The 49ers are very different than the Seahawks when it comes to the read-option, so the Falcons will not be prepared just because they faced Seattle last week.
Kaepernick can do the same thing, and the 49ers will block for him. Clay Matthews and the Packer pass rush had no success against Joe Staley and the superb 49er offensive line, and against a weak pass rush in Atlanta, the offensive line will thrive. If Kaepernick wants to go deep, he will have time. If he needs time for someone to get open, he will have it.
And he will succeed.
The read-option is so successful because there are only one or two (usually one, if everything works) guys that can make a play quickly. If the weak-side linebacker goes in to stop the run, Kaepernick will keep it, and that will leave very little possibilities to make a play. If the weak-side linebacker tries to trap Kaepernick, and the blockers clear a path, Gore or James can burst through a hole.
It's also hard because guys like Peyton Manning and Tom Brady don't have the skill set to execute it. Most teams don't run the read-option, and while the Falcons have faced teams with running quarterbacks, they haven't run into the 49ers.
They haven't faced the tough offensive line, and they haven't seen a team exactly like the 49ers. They have a great O-line and Delanie Walker to block downfield as well, with James and Gore able to run the offense along with Kaepernick.
Doing run fakes and mixing up the play calls will also open up short passing lanes for the 49ers, and assuming that the lineman can hold up and if the end attacks the run, Kaepernick can go deep for Crabtree or Vernon Davis. He'll probably have Walker or Bruce Miller to block the originally unblocked linebacker if needed, as well as Staley, Alex Boone and others on the line.
Running the option does the exact opposite of limiting Kaepernick's skills. When executed properly, he can still throw deep and make the hard, long throws he likes to make. But he can also hand off and run the ball, and Atlanta will continue to be fooled.
Greg Roman had some trouble with the play-calling during the regular season, but he was perfect against Green Bay. He's going to keep Atlanta off-balance, and with the constant threat of Gore running as well, it would be ludicrous to change things up now.
Because if they did, it would cost them a trip to New Orleans.