Whatever one thinks of the accomplishments (or lack thereof) of the Bill Clinton presidency, his initial campaign did succeed in making one indelible mark on American culture, giving us the quintessential expression for keeping your eye on the ball. Clinton’s early campaign mantra, “It’s the economy, stupid,” has proved wonderfully adaptable to almost any situation in the form of “It’s the [fill in the blank], stupid.” As the Mets demonstrated during the weekend, it’s a phrase of which they could make good use, in the form of “It’s the farm system, stupid.” In this roller-coaster Mets season of crash and recovery, firings and injuries, it’s the one thread that has remained consistent throughout the season.

The last game of the Astros’ highly damaging sweep of the Mets featured an inexplicable base-running gaffe by minor league veteran Robinson Cancel; a 22-year-old starting left fielder out of Double-A in Nick Evans; another Double-A outfielder, Dan Murphy, pinch-hitting (having started in left field the day before), and a reliever from Double-A, the former first-round supplemental pick Eddie Kunz, on the mound. While there’s nothing wrong with accelerating a player’s development schedule if his abilities warrant it, it’s clear that the Mets were making their choices out of a lack of viable alternatives.

Viable alternatives are what “It’s the farm system, stupid” is all about. The minor leagues have long been the single leading Darwinian determinant in baseball. Going back to the 1920s, when Branch Rickey set up the first “chain-store baseball” plan for the St. Louis Cardinals, the adoption of an aggressive minor league program quickly came to be the defining characteristic of successful and unsuccessful clubs. For underfinanced teams such as the Cardinals, it meant on-field success completely out of proportion to their revenues. For rich clubs such as the Yankees, who began their own farm system in 1932, the combination of the farm system and their ability to pay for top scouts and bonuses meant a kind of perpetual motion device for winning. On the other side of the divide, teams such as the Washington Senators and Philadelphia A’s, who reluctantly went into the prospect business either because of a lack of funds or a blind adherence to the old way of doing things were doomed to suffer years of on-field losses, off-field financial strain, and eventual extinction.

Despite the decades of evidence as to the indispensable part that farm systems play in big league success — from supplying replacements for big league talent in the heat of a race to keeping the major league payroll down — from time to time teams lapse into treating their farms as tangential appendages to the major league roster, useful only to provide fodder for trades. The Yankees spent the decade of the 1980s acting that way, with the result that they fielded a long series of expensive, entertaining, star-laden, veteran teams that won a lot of regular season games but were never good enough to reach the postseason.

The Mets are at that stage now, through an interesting series of conflicting assessments and imperatives. General manager Omar Minaya’s job is to stock the roster as best he can. Aside from the occasional great success like 2001 first-round/supplemental pick David Wright and the greatly improved Mike Pelfrey, the ninth overall pick in 2005, the Mets have been very mediocre at drafting a development team. They haven’t hit the lows of the 1990s, when they annually tossed away high picks on flawed players such as Al Shirley, Ryan Jaroncyk, and Robert Stratton, but they haven’t produced many players of use, and what has been produced has been flawed. As Carlos Gomez has demonstrated for the Twins, for all his physical assets, he is, at least for now, not a major league regular. His range in the outfield has been extraordinary. His work at the plate has been extraordinary, too, but not in a good way. Any general manager would have hung up the phone with the Twins and said, “They want to give me Johan Santana for a package built around that guy? I’d better jump on that.” Minaya can’t be blamed for cashing in his team’s near-trash for another’s undisputed treasure.

Yet, this deal, as well as more questionable ones such as that which sent Lastings Milledge to Washington for Brian Schneider and Ryan Church, when combined with an extremely aged roster, left the cupboard bare. At the outset of the season, it was said by many analysts (including this one), that the Mets lacked the depth to survive a hangnail. That was wrong — they can clearly survive a hangnail. Their ability to withstand more than that it still in doubt.

Whatever the end result of this season, even if the Mets do qualify for the postseason, there will be plenty of blame to go around for what should have been a cakewalk in a weak division. Much attention will be paid to the shortcomings of the major league roster, but the Mets would have been better able to react to injuries and poor performances if they had had more depth to work with in the first place. In other words, it’s not just Omar: It’s the farm system, stupid.

Mr. Goldman writes the Pinstriped Bible for yesnetwork.com and is the author of “Forging Genius,” a biography of Casey Stengel.