J.J. Abrams' best Star Trek callback in his first Kelvin Timeline movie was actually entirely unintentional, and that actually makes it far more perfect. In 2009, J.J. Abrams rebooted the story of Star Trek: The Original Series by introducing an alternate timeline - known as the Kelvin Timeline - in which James T. Kirk grew up without a father due to a Romulan attack on the USS Kelvin. So far, Star Trek's Kelvin Timeline consists of three movies, with a fourth reportedly in production.
One of the most obvious differences between the Kelvin Timeline movies and the Prime Universe's is the rebooted cast, each of which offers their own spin on their iconic The Original Series characters. The first film in Abrams' continuity, simply titled Star Trek, establishes how James T. Kirk and his crew first met, and how he came to be in command of the Enterprise. Acting as an alternate origin of sorts, 2009's Star Trek was positively packed with references to various moments from the franchise's long and storied history.
Perhaps one of the most subtly brilliant of these comes in the scene in which Chris Pine's Kirk is seen taking the infamously unwinnable Kobayashi Maru test. The test was never shown in The Original Series or its movies, but in Star Trek II: The Wrath of Khan, Shatner's Captain Kirk describes how he beat the test by reprogramming it (or cheating, as it's better known), eating an apple as he details his unprecedented accomplishment. In Abrams' Star Trek, Chris Pine is eating an apple while taking the test, making the moment seem like an obvious callback to the scene in Wrath of Khan. However, Abrams has since said that the apple callback was entirely coincidental - it was included simply to add to the tone of the scene, and wasn't intended as a reference to The Wrath of Khan.
The Kelvin Timeline's James T. Kirk eating an apple while taking the Kobayashi Maru came about simply because J.J. Abrams was once told that it made an actor look cocky. Wanting Pine's Kirk to look self-assured during the scene, Abrams had him eat the apple blissfully unaware of the perfect callback he was creating. This created the appropriate air of overconfidence necessary to convey Kirk's knowledge that he'd already beaten the test, and it accidentally proved to be a near-perfect connection to Star Trek II: The Wrath of Khan.
However, it's not just the parallel between the scenes that makes the callback great, but the coincidental nature of it, too. The idea that something so perfect could happen by pure coincidence seems to perfectly match the character of Star Trek's James T. Kirk, whose ability to narrowly escape even the direst situations borders on the uncanny. The notion that such an excellent callback simply fell into place adds a real-life layer to the constantly growing legend of the beloved Star Trek character. As the callback ultimately stemmed from J.J. Abrams' desire to make Chris Pine's James Kirk seem every bit as cocky as William Shatner's, it's only fitting that it inadvertently became Star Trek's best and most subtle reference to the Prime Universe.