After 2012, however, the contract status of players and the state of the team will change. Some Niners will underperform. Others will outplay their contract and feel they can get more elsewhere.
Among the players with deals expiring at the end of this league year are Isaac Sopoaga, Larry Grant, Ricky Jean-Francois, Delanie Walker, Randy Moss, Dashon Goldson, Brandon Jacobs, Tramaine Brock (restricted free agent), Ted Ginn Jr. and Tavares Gooden.
Several starters and key players are in this group, so San Francisco will need to prioritize because it won’t be able re-sign all of them. Moss and Jacobs should be expected to depart, but don’t be surprised if Walker and/or Ginn Jr. go, too.
The 49ers will also have to make a decision at nose tackle. With the expiring deals of Sopoaga and Jean-Francois, the Niners may make a surprise move if No. 90 demands a high salary. Jean-Francois, a fourth-year defensive lineman from LSU, will be wrapping up his rookie deal at the end of 2012.
Jean-Francois has successfully filled in during the regular season. He is the first defender to get reps at any position on the line, either as a sub or starter. He has fared well in his few career starts. As a result, there is little drop-off when one of the three regular starters needs a breather.
It seems that the 49ers will be in for another decision-filled offseason in 2013.
Ways the 49ers Can Save Money
Alex Smith 2013 salary: $9.75 million ($2.25 M in bonuses).
Colin Kaepernick 2013 salary: $1.29 M.
A lot of 49ers fans are anticipating this seemingly inevitable transition.
Colin Kaepernick was a high-profile NCAA passer from Nevada-Reno, that QB guru and rebuilding head coach Jim Harbaugh hand-selected for his team. With the second overall pick in the Harbaugh era, San Francisco brought in the next potential franchise quarterback.
The the 49ers could be ready to start Kaepernick in his third year as a pro.
That would explain the reasoning behind Alex Smith’s short-term deal, and why the team was sniffing around Peyton Manning. The Niners can opt out of Smith’s deal at the end of this season and move into the Kaepernick era.
If Smith plays in 2013, he will be the highest-paid player on the 49ers' roster. If San Francisco elected to make the transition in the coming offseason, it would save the team more than $8 million.
Of course, a significant move at the quarterback position depends heavily on how the 49ers finish in 2012.
49ers linebacker Parys Haralson will be owed a base of $2.57 million in 2013, and it appears likely that the team will finally cut ties with the veteran defender. And whether or not Haralson was healthy this year, Aldon Smith edged ahead of him when he transitioned into the starting role.
It seems a parting of the ways could be in the not-too-distant future.
Additionally, San Francisco expects to have 2012 draft pick Darius Fleming, who was on the injured reserved list this year after an ACL tear. The former Notre Dame linebacker is ahead of schedule and could reasonably assume backup duties.
Entering the second year of his rookie contract, Fleming is set to earn $521,000—more than $2 million less than Haralson’s contract. By going younger, the 49ers would save themselves an unnecessary hit against the cap and still be satisfied with the depth provided by Fleming.
Meanwhile, OLB Darius Fleming, who is ahead of sked from an ACL tear, will remain on PUP for the rest of the season. #49ers.— Matt Barrows (@mattbarrows) November 6, 2012
The 49ers' highest-paid offensive lineman is center Jonathan Goodwin, who is set to earn $5 million in 2013. It will be the third and final year of his contract, after coming over from the New Orleans Saints.
In the past two drafts under Harbaugh and Trent Baalke, the team has brought in a number of offensive- line prospects. This coming offseason could be the year the team opts out of Goodwin’s contract, which includes $1.36 M in bonuses and transition to one of the young bucks.
Among the top candidates to compete for the starting center job in 2013 are Joe Looney and Daniel Kilgore.
Kilgore was the first offensive lineman drafted in the Harbaugh era, coming to the team in 2011. Kilgore, like many other 49ers draftees, has been in an understudy role, but he could be the closest to being game-ready.
While Looney, a mid-round pick in ’12, projects as a guard, he may have the higher ceiling of the two.
Kilgore will earn a salary of $595,650 in 2013, while Joe Looney will pull in $586,250. Going with either player could save San Francisco $4.5 million against the cap.
State of the Cap
Entering the 2012 regular season, the 49ers sat at the bottom of the league in terms of cap space, with $880,000 remaining, per Pro Football Talk. For scale, the Eagles lead in cap space with $21.4 million, while the league average is $7.53 million.
Of course, the cap situation changes annually. The 49ers' biggest hit this year comes with Patrick Willis earning a salary of $17.64 million. He will make more in 2012 than the No. 2 and 3 earners combined: Alex Smith ($9.25 M) and Vernon Davis ($8.02 M).
In 2013, six of San Francisco’s top-10 earners will be on offense. That list includes their top skill players: Alex Smith, Vernon Davis, Frank Gore, Michael Crabtree and Mario Manningham. Former Pro Bowl center Jonathan Goodwin will also be among the highest-paid 49ers.
As a result of great coaching and talent acquisition, San Francisco also has a number of players outperforming their contracts. It is only a matter of time before the 49ers come to a crossroad with NaVorro Bowman, Dashon Goldson, Alex Boone, Tarell Brown and Delanie Walker.
When it comes to evaluating, managing and retaining talent, Baalke and Paraag Marathe are quite the tandem.
Marathe has been with the 49ers for more than a decade, but just entered his second year as the organization’s chief operating officer. Marathe’s role includes being “the club’s chief contract negotiator and salary cap architect,” per 49ers.com.
With Baalke’s input, San Francisco was able to accomplish great things in the past two offseasons.
Roster Situation, Needs and Priorities
The 49ers' departures in 2013 will free up space on the depth chart for players like A.J. Jenkins and LaMichael James. The holes left by Randy Moss and Brandon Jacobs will not necessarily make the team desperate in free agency.
But with only four wide receivers under contract in 2013, it could once again be a focus in the draft, which would be a financially efficient way to handle the matter. Like the past two offseasons, the 49ers will be looking for depth and high-ceiling, project players, not starters.
And whether it’s the draft or free agency, San Francisco will continue to operate under the radar.
Since there will not be a lot of starting roles available, the 49ers won’t be reaching for players beyond their set price tag. In fact, there should be a lot of focus on retaining their players, rather than seeking pricey free agents or trading up for overrated players.
Among the priorities are defensive starters Goldson and Sopoaga. Goldson is having another Pro Bowl year and could be named an All-Pro in 2012 at this rate. Though reckless, he is becoming a fan favorite and more consistent overall player.
Sopoaga, another starter, will also require a deal. The stat sheets will not indicate a big payday, as Sopoaga plays the unglamorous position of nose tackle. The 49ers could move ahead unscathed with Ricky Jean-Francois, but they might not want to.
This decision will be interesting.
Even more so, the team will want to extend Bowman, who is coming to the end of his rookie contract soon. He should be in line for a big payday after being named an AP All-Pro after a breakout performance in 2011. And even though the Niners run a 3-4 scheme, one could argue that it’s not financially sensible to pay two All-Pro inside linebackers at face value.
Getting this sort of deal done would likely require other players taking pay cuts, unless the 49ers can exercise other options like the scenarios mentioned earlier.
The 49ers are in a position to free up a good amount of cap space, but they will need to make sacrifices and perhaps an unconventional decision or two. A big theme in the coming offseason could be the team going younger, which in turn, could save the team quite a bit of money.