The San Diego Padres’ firing of general manager Josh Byrnes on Sunday ended his depressing run of two-plus losing seasons, leaving behind one of the worst teams in baseball and one of the worst offenses of all time.

The Padres went 76-86 in each of Byrnes’s first two seasons at the helm, then fell to 32-43 this year — 12.5 games out of first place — before his ouster. This season, they averaged less than three runs scored per game, and were shut out a major league–high 11 times. They ranked last in batting average (.214), on-base percentage, slugging, and park-adjusted offense. San Diego’s .274 on-base percentage entering Sunday’s game was the lowest for any team in the past 100 years.

Byrnes made lots of mistakes in his relatively short time in charge, but his firing only begins to address the team’s problems. The Padres are an undercapitalized team, screwed by shady owners and playing in a division with two financial powerhouses. They’ve been completely clueless on how to build a winning team at Petco Park since the day it opened. They’ve given too much money to players who tanked, bid farewell to others who’ve flourished elsewhere, and generally chosen the wrong guy nearly every time they’ve faced a major decision this century. And they’ve been unfathomably bad at scouting and player development for decades, having failed to draft and develop any hitters who’ve become stars in San Diego since the late Tony Gwynn.

Byrnes’s list of missteps starts with the Mat Latos trade of December 2011. Latos had emerged as one of the best young starting pitchers in the league when the Padres shipped him to Cincinnati. The returns thus far have been awful: Catcher Yasmani Grandal has a 50-game suspension under his belt and has yet to develop into anything close to the impact offensive player the team hoped he’d become (he’s hitting .195 this year); right-hander Edinson Volquez, now with the Pirates, couldn’t find the plate if he threw from five feet away; and first baseman Yonder Alonso has been the sixth-worst hitter in the majors this year, confirming the worst fears of skeptics who saw weak power for a first baseman and projected poor results.

The acquisition of Alonso created a first-base surplus that Byrnes felt compelled to address. Only Byrnes unloaded the wrong guy, trading Anthony Rizzo to the Cubs and keeping Alonso. Rizzo has developed into a cornerstone player in Chicago at age 24, while the 27-year-old Alonso is working on the second-worst offensive season put up by any first baseman in the past half-century. The Padres did get Andrew Cashner back in the Rizzo deal, and he’s pitched well after an injury-plagued 2012 season started his career as a Friar. Then again, Cashner just hit the disabled list with a shoulder injury, and his track record of health problems has cast doubt on the prospect of a speedy return.

The rush to trade Rizzo looks even weirder given how Byrnes handled a similar situation at catcher. After acquiring Grandal, Byrnes gave fellow catcher Nick Hundley a multiyear contract in March 2012. Though the deal only guaranteed three years and $9 million, it’s turned into a bust anyway, one that combined confusing process (committing to Hundley right after acquiring Grandal) with terrible results (Hundley has batted just .210/.261/.333 since signing the deal, worse than any catcher with as many plate appearances except the offensively inept, defense-first Rays receiver Jose Molina). Hundley was traded to the Orioles last month, and you could argue that Grandal is also extraneous, since the Padres have Austin Hedges — a 21-year-old catcher with elite defensive skills — playing at Double-A.

Then again, so many supposedly promising Padres prospects have busted over the years that it’s now tough for fans to have much faith in anyone. Second baseman Jedd Gyorko looked like a keeper after breaking into the majors by swatting 23 homers last year, finishing sixth for NL Rookie of the Year honors in a crowded field. This year, he’s been atrocious, batting .162/.213/.270 — worse than any other hitter by a wide margin. Cross your fingers that this is just a terrible sophomore slump, a fluke caused by a .192 batting average on balls in play, or some combination of temporary, curable struggles, because the Padres already committed six years and $31.5 million to Gyorko. If he fails to bounce back, Byrnes will end up 4-for-4 on multiyear deals for young players who failed to pan out, with Gyorko joining Hundley, center fielder Cameron Maybin (a .242/.302/.354 line and just 207 games played since signing a five-year, $25 million extension in March 2012), and Cory Luebke, a promising left-hander who got $12 million guaranteed, made five starts, went in for Tommy John surgery, and hasn’t pitched in more than two years.

With so little front-line talent on the roster over the past two-plus seasons, deciding what to do with a player who actually put up numbers became a problem too. Chase Headley posted a career year in 2012, one built mostly on an out-of-sight second half in which he hit .308/.386/.592 (he batted a more modest .267/.368/.413 in the first half that season). The Yankees were one of several teams in dire need of third-base help that might’ve made an aggressive trade offer for Headley. Instead, the Padres offered Headley a contract extension, got turned down, shrugged, and watched as his value disappeared; he’s hitting .201 this year, while fighting through a herniated disk in his back.

Predicting how young players will develop is one of the toughest tasks any GM will face, and even the sharpest operators will make major mistakes — see Billy Beane with Carlos Gonzalez, Andre Ethier, and Carlos Pena, or John Schuerholz with a young Jermaine Dye, and many others. More damning were some of the mistakes Byrnes made in evaluating established major league talent. He traded for Carlos Quentin on New Year’s Eve 2011, then signed the righty-swinging outfielder to a three-year, $27 million deal, hoping to lock up a middle-of-the-order power bat to lead a Padres renaissance. Instead, Quentin has seen nearly as many doctors as he has fastballs, never playing in more than 86 games in a season as a Padre; those who watched Quentin struggle with injuries every year with the White Sox were shocked (SHOCKED!) to see him keep getting hurt as he aged into his thirties. In his defense, Quentin has put up mostly solid offensive numbers when he’s managed to stay upright (other than hitting .185 this year in limited action). Then again, he’s given a lot of that value back via awful defense.

As many slipups as Byrnes has had, he did have some successes, too, most notably in buying low on Tyson Ross, Ian Kennedy, Seth Smith and other scrap-heap finds who became useful players in San Diego. Also, some of the team’s failures have been due to bad luck. Though you can certainly blame Byrnes (and his predecessors) for lousy performances by Padres players, the swarm of injuries that’s hit this team over the past few years would’ve been tough to foresee. A Tommy John epidemic list claimed Luebke, who looked like one of the best young lefties in the game in 2011; Joe Wieland, a promising young right-hander; Casey Kelly, one of the main pieces in the big Adrian Gonzalez trade with the Red Sox in 2010; and several others. All told, the Padres have lost more days to DL stints over the past four years than any other team.

Moreover, the Quentin debacle looks all too familiar. Committing to an injury-prone slugger with a wooden glove is exactly the kind of move that’s defined the Padres’ decision-making for many years. Craig Elsten, who’s covered the team since 2000, highlighted the scope of the Padres’ poor planning and the masterful job they’ve done of turning their home ballpark into a major liability.

“In 2002 I was given a walking tour of the new park,” Elsten said. “In all of the lead-up interviews, we had been told Petco Park would play ‘fair’ and may in fact favor left-handed hitters! The engineers believed there would be a jet stream to right-center, which played into their decision to put the right-center field wall a half-mile away. We walked in through the left-field bleachers and saw the new field for the first time, and I shouted in disbelief. I told my partner Ben, ‘This is going to be the biggest pitchers’ park in baseball!’ [Then GM] Kevin Towers was there and said, ‘No, the ball’s going to fly out to right.’ In the second night game at Petco Park ever in 2004, the fog rolled in from the bay in the late innings. It was like a white smoke monster coming over the top of the park from behind home plate. The fog came in to center field, stopped, and turned straight down. It was Mother Nature telling everyone what really happens to something in the air at this park.”

Elsten is one of many Padres followers who believes that the team has taken the wrong approach to the smoke monster, trying in vain to fight it, instead of embracing it. They’ve put their faith in players like Quentin (along with Phil Nevin, Ryan Klesko, and other slow, defensively challenged mashers) while watching athletic speedsters come to town and wreak havoc. When Dee Gordon came to town last weekend he made that kind of impact, at one point turning a shallow single into two runs, driving in one, then manufacturing another by taking three bases with his legs.

As Elsten put it: “If I could set the Padres’ direction organizationally, I’d put up a bunch of posters of the 1985 Cardinals in the office. Build me that and watch this park come alive.”

Adopting that kind of cohesive strategy could be a major challenge, given who’s in charge, what those in charge have done (and not done) over the years, and how little money the Padres are willing and able to spend.

The most obvious problem has been the draft. The following is a list of first-round picks the Padres made from 1994 through 2009, along with each player’s career Wins Above Replacement:

See those blank spaces in the WAR column? Those represent players who never got into a single big league game. It’s a murderers’ row of failure. For years, former team owner John Moores hamstrung the team’s scouting budget and refused to invest real money in premium draft talent, resulting in lackluster picks like Nick Schmidt and Allan Dykstra. On the rare occasions when they’ve spent real money, they’ve still whiffed, such as when they gave Donavan Tate $6.25 million in the hopes that he could go from raw athlete to major league success story (didn’t happen). And of course there was the coup de grâce: Matt Bush as the first pick of the 2004 draft, as Moores handpicked the local kid over Jered Weaver and Stephen Drew (the two top targets for Towers and Padres scouts), along with Justin Verlander and a bunch of other first-rounders who became legitimate big leaguers. A decade later, Bush is not only one of the biggest busts in baseball history, but also a convicted felon. Getting this little production out of 18 first-round picks, seven of them in the top 10, is a great way to crush a franchise.

The Matt Bush disaster has been dissected so many times at this point, Padres fans now wince at the mere mention of his name. The more relevant common denominator here is an ownership and upper management group that’s made a mess of things for far too long. There were the years of meddling and cheaping out on the draft. The limits placed on major league spending, which is how the Padres ended up Dumpster diving for the likes of Jeff Suppan and Jason Marquis, and gambling on a huge-risk commodity like Josh Johnson, rather than acquiring real talent. The $200 million in TV money that Moores and his partners were allowed to take on their way out when they sold the team.

Moores is gone, as is his short-lived successor/predecessor in the owners’ box, Jeff Moorad. But much of the old guard remains. Ron Fowler’s been involved with the ownership group since the ’90s and is now the face of the franchise. Mike Dee spent eight seasons with the Padres, left in 2002, then returned last July to take over as president and CEO. Continuity is often a good thing when you’re trying to build a winning organization. But in the case of the Padres, one of baseball’s least successful franchises on and off the field, having some of the same guys running the show could turn out to be a bug, not a feature. Dee in particular has presided over some head-scratching moves in less than a year in charge, from letting a popular public-address announcer go to drafting Johnny Manziel to making recent public statements expressing surprise over the team’s poor play. None of these instances bring major implications by themselves. But Dee already had to fight against negative perception of the team’s direction when he took over, and Padres fans haven’t seen much to make them feel better about the team’s future since then.

Dee’s next task will also be his most important: hiring Byrnes’s successor. Already, the speculation has begun as to who will take the reins, with a combination of old and new faces being cited as candidates. The farm system has potential, and we’re at the point when fans can get excited about unexpectedly great major league debuts, because what else is there to crow about?

Still, whoever claims the Padres GM’s chair will face a monumental challenge: making the right moves to turn around one of baseball’s most moribund franchises, and hoping his bosses don’t screw it all up.

Thanks to David Marver, Bryant Webster, and Justin Halpern for sharing additional thoughts for this story.