Bill Belichick's team certainly showed terrific resiliency in battling back from a seemingly insurmountable 31-3 deficit, but ultimately some ugly warts revealed themselves in the humbling defeat.
First and foremost, the Patriots' No. 1 area of concern is the pass rush.
That's nothing new for Pats fans, as the defense has lacked consistent pressure for years now.
While first-rounder Chandler Jones provided a huge spark early (six sacks in his first eight games), the rookie has been shut out in his last four appearances.
Jones suffered an ankle injury against the Indianapolis Colts and missed two games. He just hasn't looked the same in his return.
The 6'5", 260-pounder hasn't exhibited the same explosive first step or closing ability that made him a leading candidate for Defensive Rookie of the Year and the Patriots' No. 1 pass-rusher.
What is the Patriots' biggest area of concern?
Besides Jones, the Patriots' pass rush has also suffered since losing designated rusher Jermaine Cunningham.
The former second-round pick out of Florida had carved out a valuable role as a three-technique rusher and backup defensive end, racking up 23 tackles, 2.5 sacks and two fumble recoveries.
Cunningham's strong season came to an abrupt halt as he was suspended four games for violating the league's policy on performance-enhancing drugs.
In order to get the pass rush back on track, Belichick and defensive coordinator need to make use of their excellent linebackers and dial up some more exotic blitzes.
Dont'a Hightower and Brandon Spikes are excellent blitzers and bring terrific size and aggression to the table.
Sending the speedy Jerod Mayo on weak-side blitzes would also help take some pressure off Jones and Rob Ninkovich.
Sorting Out the Backfield Rotation
In terms of pure talent, there's no question Stevan Ridley is the best back on the Patriots roster.
Unfortunately the second-year back may have cost himself playing time after putting the ball on the ground twice against the 49ers (one was overturned).
Although he was drafted one round later than fellow second-year back Shane Vereen, Ridley has been the work horse for New England in 2012, carrying the ball 252 times for 1,105 yards and 10 scores.
Ridley's slashing style and ability to pick up yards after contact has given the Patriots tremendous balance in their offense, but his fumbling issues must be corrected before the playoffs.
The rest of the backfield situation can be confusing, as Danny Woodhead will have games where he's the No. 1 option and others where he barely sees the field.
This isn't anything out of the norm for Belichick, but in light of Ridley's ball-security issues, it's best to figure out what the rotation will be like going forward.
Despite Ridley's four fumbles, he gives the Patriots the best chance to win and should be the primary back.
Unlike in the past, Belichick should continue to give Ridley the most snaps and let him use the final two games of the regular season to correct any technique issues that may account for the fumbling problem.
Vereen and Woodhead are solid third-down options, but Ridley should continue to be the bell cow.
Shore Up Run Defense
At first glance, New England's numbers against the run appear pretty darn good.
The Patriots are No. 11 in yards allowed per game (106.4) and have forced a league-high 18 fumbles.
However, in the second half of the season, the run defense has not been as solid as one may think.
Although they've dropped just one game since their bye week, opponents have been able to run the ball fairly consistently against the Pats.
In a narrow win against the Buffalo Bills, C.J. Spiller and Fred Jackson still racked up 150 yards and two touchdowns (Ryan Fitzpatrick added 12 yards of his own).
On Monday, San Francisco ran the ball very effectively against New England's front seven, racking up 180 yards on 39 carries.
New England's front seven features some stud run defenders in Vince Wilfork, Jerod Mayo and Brandon Spikes, but a lack of depth along the defensive line has contributed to some of the recent problems.
With Jones getting healthier by the week, Belichick should be able to count on the lengthy defensive end to set the edge and force runs back to the interior.
Belichick would also do well to get a few more bodies in the rotation to spell guys like Wilfork and Ninkovich on occasion to keep them fresh in the fourth quarter.
Luckily for the Patriots, most of their problems are easily correctable, but they can't take them lightly if they hope to make a return trip to the Super Bowl.