By Sam McPherson

It’s been well written how the San Francisco 49ers were just a few plays away from being in three straight Super Bowls under former coach Jim Harbaugh, and as the 2015 season opens, those kinds of memories aren’t going to help the team this year. Perhaps no team in the National Football League was as good as the 49ers from 2011-13, but this season will hold nothing but confusion and questions for San Francisco. Head Coach Jim Tomsula has the confidence of the organizational brass, yet he will have to win on the field to prove himself to the fan base.

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The 49ers don’t have the roster of talent they had under Harbaugh, and that’s going to be tough on Tomsula. Much of the feared defensive front seven from seasons past is gone, and offensive stalwarts Michael Crabtree and Frank Gore have departed as well. Quarterback Colin Kaepernick remains, although if Harbaugh couldn’t stop his decline over the past few seasons, perhaps no one left on the 49er staff can, either. Yes, it’s those kinds of questions that need to be answered in 2015 at Levi’s Stadium, home of Super Bowl 50, and chances are San Francisco will not be the NFC representative.

The Harbaugh Effect

Let’s just get this out of the way: It’s very probable that Harbaugh wore out his welcome in San Francisco last season. The team seemed sluggish, although it’s possible that was due to three very deep postseason runs in 2011-13. Those extra games can take their toll on a roster, especially when none of the playoff experiences end in a Super Bowl victory. Thus, the team won’t have those excuses in 2015, since they finished 8-8 last year and had the extra month of rest to recover for this season. Oh, and with Harbaugh gone, his rough edges have been replaced by a reported player’s coach (Tomsula).

The issue is that Tomsula has a tough act to follow, and he doesn’t have the talent that Harbaugh did on the roster. This is almost a no-win scenario for the new head coach. Tomsula has limited head-coaching experience (2006 in the World Football League), and although he’s been with the 49ers since 2007, it was an interesting hire for San Francisco. Tomsula did lead the 49ers briefly in 2010 after the firing of Mike Singletary, winning the final game of the season as the interim head coach. All in all, we really don’t know what to expect from Tomsula in this situation.

Defensive Deficiencies

Linebackers Chris Borland and Patrick Willis have retired. So has defensive end Justin Smith. Toss in the long overdue release of defensive end Aldon Smith last month (due to yet another arrest), and the 49ers front seven isn’t anywhere near as imposing as it was from 2011-13 when the team was dominating the NFL. Linebacker NaVorro Bowman returns from injury, however, and that at least gives San Francisco an anchor on defense—assuming he’s 100 percent healthy after missing all of last season. One could argue the 49ers demise began with Bowman’s injury against Seattle in the 2013 NFC Championship Game, in fact; it was devastating.

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Most of the 49ers front seven is now unrecognizable, and the secondary already had its issues (especially at corner). Last year, San Francisco gave up 340 points, a whopping 111 more than in Harbaugh’s first season with the 49ers back in 2011. If the team wants to return to elite status, a lot of it is going to depend on the defense getting better, and the talent just isn’t there to make that happen this fall. Tomsula’s experience as the defensive line coach for many years with the organization will help some, but not enough. Opponents may run all over the 49ers this year, and there’s not much they can do about it.

Quarterback Woes

Remember when Kaepernick was everyone’s darling? He took over for an injured Alex Smith in 2012 and led the 49ers to the Super Bowl. However, it’s been all downhill since for the bicep-kissing QB. The Baltimore Ravens exposed his problematic decision making in that Super Bowl, and his arm is a loose cannon at times. In addition, Kaepernick let fame go to his head. Instead of locking himself in the film room every offseason like Peyton Manning would, the 49ers quarterback posed naked for a magazine shoot and was in the news for all the wrong reasons.

It’s been a quiet offseason for Kaepernick this year, however, and maybe that’s a good sign he’s finally read to progress as an NFL QB. His career completion percentage (60.1) is barely adequate, and his yards-per-attempt numbers have declined each season since 2012. His TD tosses are down; his interceptions are up. The fact Kaepernick led the 49ers in the sabermetric measurement Approximate Value (AV) last season tells us all we need to know about how much the team regressed last season. San Francisco is going to be in a lot of shootouts in 2015 because of the defense, so Kaepernick better be ready to be at his best.

Replacing Crabtree and Gore

Wide receiver Michael Crabtree never lived up to expectations, but he was still the team’s No. 1 receiving threat in 2011 and 2012. He’d been surpassed by the reliability of Anquan Boldin the last two seasons, and Boldin remains with the team. Crabtree signed with the Oakland Raiders in the offseason, so the 49ers went out and got Boldin’s old teammate from Baltimore, Torrey Smith. It’s a little amusing to see San Francisco now with the two WRs that burned their secondary in Super Bowl XLVII. Smith does give Kaepernick a deep threat he’s never really had, however, and that should be enough to replace Crabtree effectively.

Losing Frank Gore to the Indianapolis Colts hurts more, however, even if the 49ers have a ready-made back to step in—Carlos Hyde. Gore led the team in rushing for each of the past 10 seasons, and he was the face of the franchise, really, despite Kaepernick’s meteoric rise and fall. Hyde is more than capable to replace Gore, as the former Ohio State star posted a 4.0 yards-per-carry mark last season. With Smith opening up the passing game for Kaepernick, expect both Hyde (and Kaepernick) to have more running room in 2015.

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Sam McPherson is a freelance writer covering baseball, football, basketball, golf, hockey and fantasy sports for CBS, AXS and Examiner. He also is an Ironman triathlete and certified triathlon coach.