Matthew Emmons-USA TODAY Sports

Matthew Emmons-USA TODAY Sports



During the majority of the Jim Harbaugh era, the 49ers managed to maintain a level of success few franchises could compete with.

Harbaugh's Niners went 36-11-1 from 2011-2013, and appeared in three straight NFC Championship games as well as Super Bowl XLVII. They did this in a very different manner than most teams would in the NFL during this particular era, in that they didn't have elite play at the quarterback position.

Consider that in the AFC, 12 of the last 14 teams to make the Super Bowl had either Tom Brady, Peyton Manning or Ben Roethlisbrger behind center. In today's pass happy NFL, an elite quarterback can make all the difference in the world in terms of a team's success rate.

The way San Francisco bucked this trend was by having a roster that was talented, deep and balanced at almost every position. They won games by running the ball and playing excellent defense, while getting good, mistake free play at quarterback.

From '11-'13, the 49ers finished eighth (2044), fourth (2491) and third (2201) in total yards rushing, all while throwing the fewest amount of interceptions in the league during that time frame (21).

On the other side of the ball they ranked second twice (2011, 2012) and third once (2013) in total defense, and allowed the fewest rushing yards overall in those three years.

How was San Francisco able to maintain such a talented roster? Good drafting and smart free agent pick ups had a lot to do with it, but they were mostly able to keep balance because they didn't have to pay their quarterback a large percentage of the cap, and could allocate the funds elsewhere.

As the Harbaugh era ends and the Jim Tomsula era begins, the franchise finds itself in a different predicament. The roster has turned over, and many of the mainstays from the recent run are gone or aging. Most of this didn't come as a surprise to general manager Trent Baalke (sans the Patrick Willis and Chris Borland retirements) and the team was prepared for the roster turnover.

Being prepared on paper and getting results on the field are two different things however, and players like Brandon Thomas, Carlos Hyde, Jimmie Ward, and Tank Caradine are unproven. It's also unknown how veteran additions like Darnell Dockett and Torrey Smith will fit in.

That's why much of the 49ers' future success will depend on one player: Colin Kaepernick.

For starters, while his deal is team friendly in the sense that it's basically a year-to-year contract, Kaepernick is still getting paid big bucks. He'll count over $15 million towards the cap in 2015, and that number will only increase as the years go on. He's being paid like an elite passer, and has to start performing like one.

Kaepernick's story is well documented at this point. He took the league by storm in 2012 after taking over for Alex Smith in week 11. His meteoric rise helped the 49ers make the Super Bowl that year, and came within 5 yards of winning it all.

As expected with any young quarterback though, Kaepernick was up-and-down the following season. He went into a funk from Weeks 2-11, averaging 154 yards passing a game while only completing 53.7 percent of his throws. He did turn it around late in the year though, and upped those totals to 232 and 61.8 over the final six weeks. Ultimately, the 49ers would return to the NFC Championship game, but three late turnovers by Kaepernick put the team in a hole they couldn't overcome.

After the late surge, many expected a breakout year from Kaepernick in 2014. Unfortunately, the season was largely a disaster. Outside distractions from the Harbaugh/Jed York fiasco no doubt played a part, but Kaepernick largely regressed as a passer.

He seemed to struggle to see the field and often broke the pocket too early. In turn, his team couldn't score points as he led the starting offense to only 29 touchdowns all year.

The offensive line was partially to blame, as poor pass protection was often the norm and Kaepernick seemed skittish possibly because of it. The 49ers allowed a sack percentage of 9.6, which was the third worse in the NFL. That number shouldn't be overly shocking though, as it was near the bottom of the league in every season under Harbaugh. They were sixth worst in 2011 (8.9 percent), third worst in 2012 (8.6 percent) and fourth worst in 2013 (8.6 percent). Still, with Daniel Kilgore and Anthony Davis returning to full health, as well as a full training camp from Alex Boone, the unit should be much improved next year if healthy.

Another issue was the fact that even though the 49ers had brand name players at wide out in Anquan Boldin, Michael Crabtree and Stevie Johnson, they were all kind of the same receiver. Each is more of a possession guy, and defenses were never worried about the deep ball. In turn, San Francisco was forced to play offense in a box, without any real threat of the big play.

With Smith now in the fold (and Vernon Davis presumably healthy), that won't be the case in 2015. For the first time in recent memory, the Niners have a legitimate deep threat, a tight end that causes mismatches, and someone to move the chains underneath in Boldin. They also have a versatile weapon in Bruce Eillington that can allow offensive coordinator Geep Cryst to get creative.

Something else that you could say hurt Kaepernick was the team's reluctance to throw to their running backs. Per Pro Football Focus, the 49ers attempted five screen passes to their running backs in 2014 (although I can't remember any of them) and the backs had 44 receptions totals.

With Reggie Bush now in the fold to go along with Carlos Hyde and Kendall Hunter, it would appear that using the running backs in the passing game will be something the team will look to do this upcoming season. Taking a check down can only help in Kaepernick's development, as 2nd-and-5 is much easier on a quarterback than 2nd-and-12.

The long and the short of it is, while some of the faces have changed, and more young players will begin to be worked in, Kaepernick still has a lot of talent around him. If he develops as a passer, there's no reason the 49ers can't be playoff team in 2015. As the years go on though, he'll have to continue to get better or San Francisco could be in trouble.

The 2016 season could bring even more transition if Boldin and Vernon Davis are no longer with the team. If younger players take their spots, they'll need a reliable veteran quarterback to continue to move the offense. Kaepernick doesn't have to be Tom Brady, but he will have to elevate his overall game to a Pro Bowl level.

Here's some food for thought though...if Kaepernick plays in 2015 the way he did last season, will he even be the quarterback in San Francisco come 2016?

Al Sacco has covered the 49ers for various sites over the years. He's been a guest on multiple podcasts and had his work used on ESPN NFL Insiders. Follow Al on Twitter @AlSacco49