There’s plenty of evidence that the Super Bowl hangover is real. Since the AFL-NFL merger in 1970, 28 of the 42 Super Bowl losers failed to win a playoff game the next season. The last Super Bowl loser to make it back the following year was the Buffalo Bills. (And the year before that, it was the Bills ... and the year before that, also the Bills.)

Who knows why Super Bowl losers fare poorly. Could have something to do with an emotional letdown. It could be subtle evidence of parity. Could be pure coincidence. Or maybe it has something to do with a shortened offseason. Playing in the Super Bowl extends the team’s season by several weeks, leaving a lot of behind-the-scenes people behind schedule.

Whatever the reason for the hangover, we’re going to analyze the football side of these Super Bowl-losing Niners. With vague signs of looming change on offense, there could be more than a few reasons that point to an imminent hangover.

OFFENSE

Jim Harbaugh and coordinator Greg Roman form the best offensive coaching tandem in football right now. In an age of finesse spread passing systems, these two have led an old-school running team to an NFC Championship Game appearance and then a Super Bowl in their first two seasons. The Niners might be the only offense left that lines up and implicitly says, "Here’s our run game; try to stop it." Last season, according to Football Outsiders, they used some combination of two-back or two-tight end sets on a league-high 48 percent of their snaps. They used sets containing both two backs and two tight ends 24.2 percent of the time, far and away the most in pro football. (This was actually the formation from which a lot of their downfield deep shots came.)

Though the Niners line up with obvious intentions to run, it’s not always clear how they’ll run. Harbaugh and Roman take a very intellectual approach to a lot of their ground designs (the Stanford influence?), focusing heavily on scheming advantageous angles for blockers and runners. (Roman likes to say, "Geometry doesn’t have bad days.") Their unconventional designs constantly create unexpected running lanes out of unconventional formations or blocking patterns.

In building a ground-oriented offense, Harbaugh isn’t just catering to the throwback values he learned from his old mentor, Bo Schembechler; he’s also catering to his personnel. The Niners have a consummate workhorse back in Frank Gore. And they have perhaps the meatiest offensive line in the league. At right tackle is the steadily progressing Anthony Davis, who got a five-year, $37.3 million contract in the offseason (with a collective $7.25 million worth of annual de-escalators if he fails to complete workouts or make weight requirements). At right guard is Alex Boone, a 6-8, 300-pounder with improved lateral mobility in the run game. At center is a veteran stalwart, Jonathan Goodwin, backed up by 308-pound third-year pro Daniel Kilgore. And, of course, rounding out the front five is the best left side blocking duo in the NFC: Mike Iupati at guard and Joe Staley at tackle. Iupati, though still too inconsistent in pass protection, has an uncommon ability to maintain balance while delivering powerful jabs on the move. Staley, one of the game’s smartest pass protectors, is an equally voracious run-blocker in space.

San Francisco’s rushing attack is as deep as it is diverse. The line has acceptable depth with last year’s developmental fourth-round guard, Joe Looney, and veteran Adam Snyder, who is capable of playing guard or tackle in a pinch. The backfield has outstanding depth, as Kendall Hunter, assuming he’s fully recovered from last year’s Achilles injury, offers more change-of-tempo juice than the surprisingly still-spry Gore. Hunter could push for 10 to 12 carries a game. Also in the mix is diminutive slasher LaMichael James, who has carved out a niche given that he’s the only back with the speed to consistently turn the corner and operate from single-back sets. The Niners also have a short-yardage back, Anthony Dixon, though with a reliable fullback like Bruce Miller there’s no reason Gore or Hunter couldn’t move the chains in these situations, especially considering that both run low to the ground. Originally, Harbaugh installed a run-oriented system to not only highlight his team’s strengths but also to mask the weakness at quarterback. As nice a guy as Alex Smith was, he had very distinct limitations as a dropback passer. That’s why the decision to bench him for second-year wonder Colin Kaepernick really wasn’t a hard one.

This is where San Francisco’s identity dilemma comes into play. Harbaugh must decide how much he wants to tailor his system to Kaepernick. Theoretically, he could keep the same run-first approach. As we saw last year, Kaepernick’s agility and long-striding speed actually add a potent dimension to the ground game. However, as we explored in the Redskins preview, the read-option could soon wane across the NFL. The Niners already saw firsthand in the Super Bowl how defenses are going to react to the novel tactic moving forward: constant, ferocious hits on the quarterback. Kaepernick, highly exposed with his upright running style, was lucky he did not get knocked out of that game.

What the Niners also must consider is that in keeping Kaepernick in a controlled, run-first system, they’d be leaving a lot of raw quarterbacking talent uncooked. Great as Kaepernick is as a runner, his lanky build and rubbery, quick-snapping arm make him an even more enticing passer.

There isn’t a clear-cut decision for San Francisco to make here; a progression passer can still be a little bit of a runner. Currently, Kaepernick as a progression passer is still more than a little bit of a runner. That must change at some point.

As they did with Alex Smith, the Niners last year confined Kaepernick to a lot of simplified either/or reads. He generally had no more than two reads, and on most dropbacks, it was one. If the initial reads weren’t open, he tucked and ran. Kaepernick thrived with this, in part because defenses had never seen him in person or on tape. He won’t catch anyone by surprise this season. It stands to reason that the unpolished elements of his game—and there are several, including presnap awareness, huddle tempo, progression passing, route anticipation and a few minor glitches in his mechanics—will be more of a problem.

Of course, Kaepernick had time this offseason to work on his shortcomings. But even if he has made progress, he may not reap the benefits in 2013. With Randy Moss gone, tight end Delanie Walker now a Titan and Michael Crabtree out with a torn Achilles, the Niners are minus three enormous facets of their passing attack. Moss was close to washed up, but for whatever reason defenses still played a safety over the top against him. Roman gladly drew up route combinations that took full advantage of that. Walker had the capacity to line up anywhere and create matchup problems, either for himself or, more often, for teammates. This was critical because Roman loves to incorporate shifts and wrinkles in his formations. (And not to be overlooked was Walker’s equally significant impact on the run-blocking designs.) Crabtree was the playmaker. He didn’t have great speed, but his body control and route running were near perfect. By season’s end he’d become one of the most clutch chain-movers in the NFL.

The Niners are hoping they’ve found replacements for all three of these weapons, but nothing is guaranteed. They did not originally plan for Anquan Boldin to be their new Crabtree—they traded a sixth-round pick for the 32-year-old receiver before Crabtree’s injury—but that’s how it will be. At tight end they drafted Vance McDonald in the second round with hopes that he can be the new Delanie Walker. At Rice, McDonald often seemed as if he was playing with oven mitts on. While he did line up at a litany of positions, it takes several years to develop the fine-tuned nuances that had come to make Walker’s game unique.

As for replacing Moss, the hope was that last year’s first-round pick, A.J. Jenkins, could fill the void. It didn’t take long for that hope to evaporate. The man San Fran traded Jenkins for, Jon Baldwin, is more accomplished but by no means a deep threat. The former first-round Chief has circus catch ability but a disconcerting sluggishness in his downfield movement (think running in sand). In fact, Mario Manningham (coming off an ACL injury) may wind up being the No. 2 receiver if he can get healthy. Or even slot man Kyle Williams (also coming off an ACL). Or former Dolphin Marlon Moore. Or fourth-round rookie Quinton Patton, though he may have too limited of a route tree having only lined up on the right side at Louisiana Tech.

The only truly familiar outlet for Kaepernick is Vernon Davis, who is a sensational athlete but constricted route runner (it’s pretty much the seams and maybe a deep cross or two; certainly no option routes for the eighth-year pro). Davis’ heart as a run-blocker has turned him into an admirable all-around tight end, though there’s been talk of playing him more at a true wide receiver spot this season.

Just how sweeping the passing game changes are may hinge on where the Niners feel Kaepernick is in his development as a progression passer. If there are limitations at receiver, it will be harder for Roman to generate easy completion opportunities through one-read designs.

DEFENSE

Somewhat quietly (or as quietly as possible for a team in the Super Bowl spotlight), San Francisco’s vaunted defense wore down at the end of last season. Perhaps this was a consequence of coordinator Vic Fangio’s infrequent substitutions (practically the only sub-package he used was nickel, which had just one personnel change, cornerback Chris Culliver replacing nosetackle Isaac Sopoaga). Not coincidentally, the defense’s late troubles coincided with the decline of its four-man rush.

After having 28 sacks over the first 11 weeks of the season, the Niners had a measly 14 in the last eight weeks (including the postseason). With less pressure generated up front, San Fran’s back seven suddenly had trouble holding up in man-to-man, which is their coverage foundation.

Deep Dive

Everything you need to know about all 32 teams and their prospects for the 2013 season, courtesy of Andy Benoit. The last four teams roll out this week.

Another non-coincidence is that the pass rush’s slide coincided with defensive end Justin Smith’s shoulder injury. It’s been well-documented: Smith, in and of himself, is not a big-time pass rusher (three sacks last season; career high is 8.5), but his brilliance in drawing double-teams and destroying protection walls with crashes and stunts creates invaluable attack lanes and favorable one-on-one matchups for teammates, most often Aldon Smith.

The Niners have recognized that the soon-to-be 34-year-old Justin Smith is indeed mortal. The two-year contract he signed in June is intended to be the final one of his career (and he may not play out the final season). In April general manager Trent Baalke spent a second-round pick on Tank Carradine, who figures to be Smith’s understudy. Before that, Baalke signed ex-Chief Glenn Dorsey, who could push for a long-term role. Ideally, Dorsey and Carradine won’t have to play much in the meantime, as Smith, recovered from his triceps injury, and the feloniously underrated Ray McDonald can remain dominant every-down forces up front. They’ll be especially critical on running downs, given that new starting nosetackle Ian Williams has played just 39 snaps in his two-year career. (It’s worth noting that the Niners at least seem to be high on Williams, as they let free agent Sopoaga walk and, despite a wealth of picks, did not address his position in the draft until Quinton Dial in round five.)

Just going off skill set, starting outside linebackers Aldon Smith and Ahmad Brooks shouldn’t be easily neutralized no matter how the defensive ends/tackles alongside them are playing. The supple Smith has freakishly long arms and frighteningly strong hands. Brooks is an explosive, unsuspectingly well-rounded athlete. Both have dynamic speed.

In 2012 the Niners carried only one scantly used backup outside 'backer on their roster (Clark Haggans, now out of the league). By season’s end Smith and Brooks had both played around 1,200 total snaps and may have been dragging. There will be chances to keep them fresher this year, as there’s newfound depth with third-round rookie Corey Lemonier coming aboard.

The Niners also took measures to improve their secondary. Chris Culliver was actually progressing nicely as the nickel outside corner. Aside from the big touchdown he surrendered to Jacoby Jones, the then-second-year pro had a very good Super Bowl (the Ravens just happened to make a few spectacular plays at his expense). Nevertheless, the temptation to sign Nnamdi Asomugha on the cheap was one Baalke couldn’t resist. (The move proved extra beneficial after Culliver tore his ACL early in training camp.) Asomugha is no longer considered an upper-echelon corner after two disappointing years in Philadelphia. But in returning to the Bay Area (he spent his first eight seasons with Oakland) he is returning to the two-man base scheme that suits his press-boundary style. Asomugha won’t beat out solid seventh-year pro Tarell Brown for a starting job, but he should get plenty of nickel work outside, with Carlos Rogers sliding to the slot. Also in the mix is Trumaine Brock, talented but troubled ex-Buc Eric Wright and incumbent backup Perrish Cox.

At safety, the departure of Dashon Goldson hurts, particularly in run defense, where he and Donte Whitner were like dual missiles firing down from the third level. Whitner is back at strong safety, while first-round rookie Eric Reid is being counted on at free safety. Unsure if they’d be able to draft the LSU playmaker (or risk-taker), the Niners had previously signed Craig Dahl in free agency. That leaves them with improved depth, as Dahl, though not as athletic or fast as blitzing specialist C.J. Spillman, has 42 games of starting experience in a variety of systems.

Saving the best for last, what allows this man-based defense to eschew complicated tactics and just focus on playing with speed and aggression is having a pair of superstars in the middle. Patrick Willis and NaVorro Bowman are the two best 3-4 inside linebackers in football (who is 1 and who is 1-A is a matter of personal preference). Both are sensational at shedding blocks. And, though not quite blankets, both can hold up in solo man coverage. (Willis generally takes the tight end, Bowman the running back.) That gives Fangio freedoms most coordinators don’t have.

Venture into the middle of the 49ers' defense—right into the arms of NaVorro Bowman (left) and Patrick Willis—at your own peril.

SPECIAL TEAMS

The Niners can only hope that their newly signed veteran kicker, Phil Dawson, works out better than the last one, David Akers. At punter, they have nothing to worry about; three-time All Pro Andy Lee remains one of the best. In the return game, LaMichael James can handle kicks. The team is hoping he can also handle punts, but if he can’t, Kyle Williams—now more than 18 months removed from his 2011 NFC Championship debacle—would make the most sense on punts.

BOTTOM LINE