Although Mangini failed in his two brief stints as a head coach, putting him in a confined role is a win-win.
Mangini was part of three Super Bowl victories with Tom Brady, Bill Belichick and the New England Patriots from 2000 through 2005. So, he clearly has a better track record as an assistant to begin with.
Regarding San Francisco, the offense struggled with building consistency against defenses that presented a sound front seven in 2012, namely within the NFC West. The St. Louis Rams and Seattle Seahawks held the 49ers to under 14 points in three of four contests.
Moving outside the division and to the other physical NFC teams, the Minnesota Vikings and New York Giants both out-played the 49ers up front. That's two more contests where San Francisco was held to under 14 points as well.
One noticeable weakness was the passing game.
Finishing ranked No. 23 in passing offense, San Francisco simply didn't attack downfield enough. Although the ground game is a strong forte, the aforementioned opponents were able to slow down the run and then force Jim Harbaugh's team into strict passing situations.
Without the run to set up play action or read-option, opposing defenses didn't honor San Francisco's aerial assault. Circling back to Mangini's potential to prepare for specific defenses, that preparation will be of immense assistance versus the more physical opponents.
As for those mentioned above, Seattle didn't present a dominant pass rush and the Rams were vulnerable over the middle and in Cover 2. The Giants were uncharacteristically weak at applying quarterback pressure and struggled in coverage as well.
Minnesota on the other hand, fielded a strong rush, but was also quite vulnerable against the pass.
These are specific defenses to prepare for because each proved capable of forcing San Francisco into a one-dimensional attack. In addition, defenses like that also field a major strength—pass rush or coverage—with a major weakness—pass rush or coverage.
It's figuring out how to decipher that aspect and then capitalize accordingly. The 49ers have the player personnel, but adding Mangini simply helps develop stronger balance to take advantage.