Kaepernick has won 17 of the 23 games he has started in the regular season and is 4-1 in the postseason. Wilson is 24-6 in the regular season with a 2-1 postseason mark.
Both were among the top 10 quarterbacks in passer rating this season and among the top four in quarterback rushing yards. Their playing style, combined with their penchant for winning, has made the Kaepernick-Wilson games anticipated quarterback matchups. Sunday's NFC championship game is the latest meeting.
"Colin's ability to run the football and throw the football extremely well, and my ability to throw the ball and run it, it's one of those things that I believe the quarterback position is changing a little bit," Wilson said. "I like to think about the 'new generation' of quarterbacks, and then you have Tom Brady and Peyton Manning on the other side in the AFC playing each other. That's a pretty interesting thing to think about in terms of if the read-option and all that is here to stay."
Both the Brady-Manning and Kaepernick-Wilson styles have been proven to work. The shelf life of the read-option in the NFL has been argued during the last two seasons, especially in Philadelphia after Chip Kelly was hired.
Neither the Seahawks nor the 49ers rely entirely on their quarterbacks' running the ball. In fact, both offenses thrive with a power running game that would excite traditionalists. But the ability of the quarterback to move - whether it's to run or throw - provides a different dimension to both offenses.
"The most difficult factor in football to deal with is a running quarterback that knows when to and when not to," Seahawks coach Pete Carroll said. "They've had the benefit of it with a lot of wins, and you can see we have, too."
Wilson said the Seahawks don't run as many read-option plays as their reputation indicates. And when he scrambles, he said, he runs to throw - not to rush. When Seahawks quarterbacks coach Carl Smith was asked what separates Wilson from other quarterbacks, he said that Wilson "moves." That does not necessarily mean run. Wilson rushed only three times in last week's playoff win.
Wilson holds the ball the longest of any quarterback in the NFL before throwing, according to Pro Football Focus. It's the by-product of extending plays. The No. 2 quarterback on the list is Foles, who is also adept at moving in the pocket to find the open receiver.
"Defenses have changed a little bit," Carroll said. "The league always adapts. The coaches are too smart, players are too good."
Wilson is averaging only 157.6 passing yards in his last five games. But he has still been able to make key plays, and Seattle has relied on a thriving rushing offense.
"Marshawn [Lynch] rushed for 150 yards. Why wouldn't you keep handing it to him?" Wilson said. "But we have a great passing game. We can do things on time, on the money."
Kaepernick's production has improved during the latter part of the season. The postseason is when he especially thrives. He has won all three of his road playoff games, and he has averaged 244 passing yards and 75 rushing yards in his five playoff games. Those exceed his regular-season numbers.
"Big stage never seems to bother him," 49ers coach Jim Harbaugh told reporters last week. "Just noticed it watching him play even going back to college, when I first started watching him play, the big games, the big challenge, the big task. He has that special ability that the great ones have to elevate their game in those situations."
That's been the case for both quarterbacks during the last two seasons. They are the headliners in a new generation of quarterbacks not because they can run but because of how often they win.
"I didn't understand how profound the statement, 'Just win, baby,' was, even when I was [in Oakland under Al Davis]," Harbaugh said. "I thought I knew, but I didn't know to the extent that I know now. Just win, baby."