Both players have faced criticism as they meet for the first time Monday night in Washington with both clubs trying to avoid a third straight defeat.
Kaepernick and Griffin led their clubs to division titles a year ago and seemed to be the kind of multi-skilled athletes that were redefining the position with the help of the read-option offence, which seemed to perfectly maximize their talents.
The 2013 NFL season may be proving otherwise.
The 49ers (6-4) were considered a favourite to return to the Super Bowl, but are 3 1/2 games behind NFC West-leading Seattle and will likely need a strong finish to gain a wild-card spot. Kaepernick is ranked 31st in completion percentage at 56.2 with only 11 touchdown passes.
''I think we are [surprised], but we still have six more to go,'' Kaepernick said. ''And we can still finish this season 12-4.''
Washington (3-7) is in last place in the mediocre NFC East. Griffin has completed 59.7 per cent of his passes with 14 touchdowns and 10 interceptions.
The quarterbacks have similarly pedestrian passer ratings with Griffin at 83.6 and Kaepernick at 81.8.
The dynamic that gave these two an edge is their running ability and Griffin ranks third among QBs with 345 yards on the ground and Kaepernick fourth at 335. While Kaepernick has three rushing TDs, Griffin has yet to find the end zone with his legs as he's coming off reconstructive surgery on his right knee.
"If you're talking about Robert or if you're talking about a guy like Kaepernick, everybody comes from different systems and when you go to the National Football League and you're working with a drop-back passing game and you haven't done a lot of that, it takes some repetition," Redskins head coach Mike Shanahan said. "Whoever has been in those shoes realizes that it doesn't happen overnight."
Kaepernick's weaknesses were evident in a 23-20 loss at New Orleans last Sunday. He was limited to 127 yards passing on a day when San Francisco was held to a season-low 81 rushing yards.
The 49ers have been unable to stretch the field with 24 pass plays of 20 yards or more for the third-worst total in the league. Things could improve Monday if wide receiver Michael Crabtree makes his season debut after being kept out by an Achilles injury.
''We'll see,'' 49ers head coach Jim Harbaugh said. ''I think he's close.''
Griffin's leadership skills have been called into question following last Sunday's 24-16 loss at Philadelphia in which his attempt to rally Washington from a 24-point deficit ended with an interception he threw off his back foot in the end zone in the final minute. He made comments that seemed to exonerate him from all blame, then clarified them Wednesday.
"I feel like for myself, moving forward, I have to be more wary of the hostility," Griffin said. "I was trying to give a compliment to Philadelphia's defence and it was taken as a shot against my coaches, [but] it wasn't."
Coaching has certainly taken its share of criticism with Washington headed for its third last-place finish in four seasons under Shanahan, who defended the direction of the franchise.
''In the future, it will get better,'' Shanahan said, ''because we do have the ability to get more depth, we've got the ability to add some players on both sides of the football and that gives you a chance to get better as a football team.''
Another lowlight during this Redskins season was the allegation by left tackle Trent Williams that an official directed profanity at him last weekend. The NFL is reviewing the incident.
The 49ers' passing game could be easy to defend since all of Kaepernick's TD passes have gone to Anquan Boldin or Vernon Davis. Davis, a Washington native who will play at FedEx Field for the second time, has reached the end zone twice in his last four games after he had six TD receptions in his first five.
Washington's passing attack also needs improvement. Griffin went 7 of 14 for 57 yards through three quarters before his final numbers improved against an Eagles defence that was playing it safe with a 24-point lead.
Both quarterbacks have faltered despite strong rushing attacks with Washington first in the NFL at 155.2 yards per game and San Francisco fifth at 141.0. The Redskins' Alfred Morris is 82 yards shy of a second consecutive 1,000-yard season.
Frank Gore ran for 107 yards to help San Francisco post a 19-11 victory Nov. 6, 2011, the last time these teams met.