Our modern criminal-justice system is designed to avoid jury trials. Through investigation and considered use of discretion, prosecutors are expected to charge only when there is sufficient evidence to convict. Once charged, defendants are encouraged to plead guilty in part to avoid a "trial penalty" — a longer sentence after a trial, often a much longer one. And 95 percent of them do just that. The Supreme Court acknowledged this reality in 2012 when it described our criminal process as "a system of pleas."

"Serial," the hit podcast about Adnan Syed's 2000 conviction for strangling his former high school girlfriend, Hae Min Lee, focuses on the question of whether Syed was unjustly convicted. Found guilty of first-degree murder and kidnapping after a five-week trial and two hours of jury deliberation, Syed is now serving a sentence of life plus 30 years. If he is innocent, this outcome is indeed a tragedy.

But if he is guilty, the result is also troubling. The average sentence for individuals convicted of murder that year in the United States was 19 years. Had Syed, then 18, plea-bargained in what his prosecutor recently described as a "run-of-the-mill domestic violence murder," he might have been able to earn his freedom by age 40.

It is noteworthy that a court is currently considering whether Syed's counsel gave him substandard legal assistance when she failed to explore the option of a guilty plea. Syed claims that he twice asked his lawyer to seek an offer from the prosecutor, but she told him none was forthcoming. The prosecutor states that she made no such request. Syed's attorney died in 2004, three years after being disbarred, before she could address this claim.

In this case, the injustice may lie not in the conviction, but in the failure to negotiate it. The unstructured presentation of the facts in "Serial" obscured a strong case for the prosecution. A former classmate who was cross-examined for five days testified that Syed confessed to the killing, as he enlisted the classmate's help in burying the body. On the evening of Lee's disappearance, Syed's cellphone pinged cell towers near the burial site. A bargaining effort should have been undertaken here.

First-degree murder under Maryland law, for a case like Syed's, requires that a killing be premeditated or the result of the commission of a felony. The prosecution's theory was that Syed strangled Lee in a 21-minute car ride after school. Strangulation, however, is not typically associated with premeditation, and the robbery, kidnapping and false imprisonment charges Syed also faced appear strained. The classmate's reliability was compromised, and the cellphone evidence was open to interpretation.

In addition, there was the mitigating factor of Syed's age at the time of the crime. Seventeen is an age of increased inclination to take risks and limited impulse control. Age, as the juvenile justice scholar Barry Feld notes, also impairs a youth's competence to make good legal decisions and participate effectively in legal proceedings. Syed needed some serious adult guidance on how to deal with the fallout of his situation.

But there is little that is systematic in our plea-bargaining processes despite the fact that they fuel our criminal-justice system. Plea bargaining is usually informal and unrecorded — sometimes simply fleeting conversations in courtroom corridors. In many jurisdictions, judges are expressly prohibited from participating in it. Attorneys for defendants plea-bargain most cases early and aggressively. But not always, and financial incentives for lawyers may lead them to do otherwise. A study conducted by the behavioral scientist James Anderson and the economist Paul Heaton in the Yale Law Journal revealed disturbing disparities in the outcomes of murder cases in Philadelphia: Public defenders achieved significantly better outcomes with fewer trials than their private court-appointed counterparts, who were paid more if the case went to trial.

A New York federal judge, Jed Rakoff, has proposed one reform: plea-bargaining conferences. In sealed proceedings, judges would examine each party's position and recommend a nonbinding plea bargain. The plan needs to be refined so it allows a defendant to opt out if he publicly acknowledges he understands what he is giving up. The proposal, however, provides a layer of review to protect the innocent from being pressured into pleading guilty, while potentially encouraging fairer plea bargains through the oversight of a neutral party. It creates a record of plea-bargaining efforts, so there can be no uncertainty as to whether an offer was requested or ignored. Finally, it might help guilty people make a more informed choice about how to resolve their cases.

In an ideal world, the primacy of the jury trial should be reinstated. Prosecute fewer people, incarcerate less often, remove the trial penalty by repealing mandatory sentencing regimes. Until then, however, we have an obligation to bring transparency and independent review to the plea-bargaining processes that decide, for the most part, who ends up in our prisons, and for how long.

JaneAnne Murray teaches at the University of Minnesota Law School. She wrote this article for the New York Times.