Heck, this offseason ESPN's Ron Jaworski said Kaepernick "could be one of the greatest quarterbacks ever", but the third-year pro has noticeably regressed in 2013, along with the rest of his team.
Here's how they can get the tremendous, talented, but struggling Kaepernick back on track.
It's not that Kaepernick's emergence a season ago was solely the product of his environment, but he was undeniably aided by a sound running game.
And that's discounting his gazelle-like read-option sprints.
Frank Gore, Kendall Hunter and LaMichael James were a highly efficient, complementary trio that kept the 49ers' offense moving.
Here's a look at how they fared in 2012 compared to this season:
|Frank Gore Yards Per Carry||4.7||4.3|
|Kendall Hunter Yards Per Carry||5.2||4.4|
|LaMichael James Yards Per Carry||4.6||3.7|
A half-yard difference is a rather substantial dip for those three.
The truly elite quarterbacks can overcome an ineffective running game, but after 11 NFL starts, it was unfair to place Kaepernick even near the elite distinction.
It's easier said than done, but to alleviate pressure from its young quarterback, a guy who's started just 17 games in his career, San Francisco must return to its dominant running ways.
With three former first-round selections on its offensive line today—and the same five Super Bowl starters—the 49ers are built to control the line of scrimmage and run the football efficiently.
Remember, Gore's quietly averaged 4.6 yards per carry on 2,086 career attempts.
Unfortunately, left guard Mike Iupati was injured in the Week 11 loss to the New Orleans Saints. His absence will make it difficult for San Francisco to bolster its running game:
Source: #49ers left guard Mike Iupati suffered a sprained left MCL. Prognosis uncertain at this point. Likely to miss *MONDAY'S* game v. WAS— Matt Barrows (@mattbarrows) November 18, 2013
Since that report, Barrows tweeted that Iupati is ruled out for the Week 12 game against the Redskins.
One of a quarterback's best friends is a consistently productive running game, and while a yards-per-carry average of 4.2 isn't terrible, San Francisco ran it much better during Kaepernick's explosion in 2012.
If a dependable running game is one of the best friends of a quarterback, a diverse and healthy stable of pass-catchers is the other.
Kaepernick needs Michael Crabtree back.
Per Mike Sando of ESPN.com, last year, Kaepernick "completed 63 of 92 passes for 898 yards and eight touchdowns when targeting Crabtree during the regular season and playoffs."
He also added, "Kaepernick targeted Crabtree 8.7 yards past the line of scrimmage on average. Seven of the 63 receptions gained 30-plus yards."
In 2012, the former Nevada standout had an Pro Football Focus (subscription required) Accuracy Percentage of 76.0. This year, without Crabtree, Kaepernick's Accuracy Percentage is 68.2.
(*Accuracy Percentage "accounts for dropped passes, throw aways, spiked balls, batted passes, and passes where the quarterback was hit while they threw the ball - factors that hurt the quarterback's completion percentage but don't help show how accurate they are.")
Losing a steady No. 1 receiver can be incredibly damaging to a quarterback, especially a young one.
Check Andrew Luck's stats after he lost Reggie Wayne.
Here's Matt Maiocco of CSN Bay Area on Crabtree's status for tonight's contest:
The 49ers did not activate Crabtree to the 53-man roster by the 1 p.m. (PT) deadline Monday, making him ineligible to make his season debut in the nationally televised night game against Washington at 5:30 p.m.
Though he managed to play in only 12 games last season, Mario Manningham caught 42 passes for 449 yards as a secondary target to Crabtree.
This year, the former New York Giants Super Bowl hero has played 72 of a possible 116 snaps the past two weeks since returning from injury.
He's snagged four passes for 38 yards.
Veteran Anquan Boldin leads the team with 47 receptions. Tight end Vernon Davis is second with 34 catches. Fullback Bruce Miller is third with 16 grabs.
The barren receiving corps is likely allowing the 49ers' opponents to sell out against the run.
Kaepernick, and San Francisco's offense as a whole, needs Crabtree and Manningham back on the field in the worst way.
If the receiving corps becomes at least marginally threatening, the running game, the defense, and most importantly Kaepernick, will be more effective.
Balance is key for a team with traditional roots like the 49ers.
Regardless of how Kaepernick played in his first opportunity as a starting signal-caller last year, his professional development was just beginning.
Was Peyton Manning a finished product midway through the 1998 season?
Will Colin Kaepernick return to 2012 form when Michael Crabtree returns?
Neither was Kaepernick in his first full season. The same goes for all young and relatively inexperienced quarterbacks.
Their maturation process takes a considerable amount of time, and it's important for teams not to ask too much of their youthful signal-callers as they're getting fully acclimated to the professional game.
With a re-dedication to the running game and especially with Crabtree returning and Manningham playing at 100 percent, Colin Kaepernick should return to the comfort zone he found himself in last year when he led the 49ers all the way to Super Bowl.