Niners offensive coordinator Greg Roman has implemented an offensive gameplan that has confused defenses who do not know whether the quarterback is going to run, hand off or pass.
Roman suggests the success of Kaepernick, who set a record for the most rushing yards by a quarterback in any game with 181 yards in playoff win over Green Bay three weeks ago, could open up opportunities to other fast and mobile quarterbacks.
"They are going to see who they have and it might tempt them to acquire an athletic quarterback that they like - it might encourage them to draft one or sign one and incorporate this into their offense," he said on Wednesday.
"People will be less apt to cross a guy off their docket in draft preparations. They will have discussions about whether they want to incorporate this into their system. Ultimately it will be exciting to see."
The man who has to work out a way to foil Roman's plans in Sunday's Super Bowl, Baltimore Ravens head coach John Harbaugh, certainly does not believe the approach is a fad.
"It will have staying power in the league, the pistol read option. The beauty of it is, and part of the genius of it is, it's such a simple idea," said Harbaugh.
"It's just a very versatile type offense and it forces you to defend a lot of different elements of the offensive attack."
There have been other variations of the read-option run in the professional game this season.
Rookies quarterbacks Robert Griffin III of the Washington redskins and Russell Wilson of the Seattle Seahawks both made it to the postseason with plenty of rushing plays, as did former Denver Broncos signal caller Tim Tebow a year earlier.
REVOLUTIONARY APPROACH
The version used by the 49ers has involved a number of different disguises and plays that can be particularly effective when combined with a quarterback like Kaepernick, who has the ability to read a defense quickly and then make the yardage.
"Greg Roman has done a job that is revolutionary in football," said Niners head coach Jim Harbaugh.
"The way he's mixed the trap, the power, the wham plays into the pistol offense and into the conventional offense has been revolutionary in many ways."
The approach is set to spread further next year with new Philadelphia Eagles head coach Chip Kelly expected to run a version of the 'read option' that he enjoyed success with at the University of Oregon.
But the performances of classical passing quarterbacks such as the Ravens' Joe Flacco, Green Bay's Aaron Rodgers, Denver's Peyton Manning and New England's Tom Brady, are a reminder that the traditional approach is still the mainstream.
Joe Theismann, a Super Bowl winning quarterback with the Washington Redskins in the 1982 season, does not see the read-option spreading beyond a few teams with athletic quarterbacks.
"It is going to be limited, based upon the abilities of the quarterback. I don't see it becoming widespread at all," he told Reuters.
Theismann believes defensive coordinators will eventually work out how to deal with the threat - just as they have with other innovations in the past.
"We saw Run and Shoot come and go. We saw the 46 defense come and go and we saw the West Coast offense, in its purest form, come and go and we saw the two tight end offense, come and go," he added.
Whether the read-option does spread to more teams or not, it is going to be fascinating to see how defensive coordinators try to nullify its impact.
"You give the (defensive coordinators) time to study something and they are going to figure out a way to make it hard," said Theismann.
Whoever triumphs in the end, 49ers quarterbacks coach Geep Chryst believes it is going to be fascinating to watch.
"We're just at the entry point of this," said Chryst. "I don't know where this is going to take us."
