Marcus' attempt to use a super ship to start a war with the Klingon Empire recalls something Weller's character in Star Trek: Enterprise, John Frederick Paxton, said. In both cases Weller takes an extreme "Us versus Them" mentality.
Beam Me Up, Scotty!: Subverted and inverted. You wouldn't think Scotty himself would make this request.
JJ Abrams and the film's writers said they didn't feel comfortable tackling an updated version of Khan. They lied. Likewise, Benedict Cumberbatch swore up and down that his character in the movie was original; and until his character was officially named John Harrison, the entire cast vehemently denied he was playing Khan whenever they were asked about it.
Leonard Nimoy said he had nothing to do with this film. He lied, as he got a cameo.
Historical In-Joke: The USS Vengeance is described as a Dreadnought-class starship, and a revolutionary new design. In Real Life, the commissioning of HMS Dreadnought, with her powerful steam turbine powerplant and all-big-gun weapons loadout led to a revolution in naval warfare, with all battleships henceforth described as being "Dreadnoughts" or "Pre-Dreadnoughts". Indeed, HMS Dreadnought is the Trope Namer for massive Game Breaker warships being called Dreadnoughts.
Interestingly, it has a second parallel with the original Dreadnought: It wasn't actually that impressive. The HMS Dreadnought only ever sunk one ship in wartime, and it was by ramming it. Likewise, despite the upgrades that went into the USS Vengeance, it is incapable of taking out a single older-model ship (The USS Enterprise).
Although in the case of the original Dreadnought, this was because there was only one major battleship battle during World War One, while Dreadnought was in port in the middle of some refits. Most of both nations' battleships were held back in reserve, the idea being not to risk such valuable assets until the enemy had committed his own.
One of Us: In a rather hilarious contrast to Robau's stern nature, Faran Tahir has been known to openly nerd out in interviews about how cool it is to play a Star Trek captain.
Reality Subtext: The central plot, involving Admiral Marcus and his plan to turn Starfleet into a more militaristic version of itself, is largely a reflection of the fandom's response to the 2009 revival; though it revitalized the Star Trek franchise for a new generation, quite a few longtime fans criticized it for emphasizing action and conflict at the expense of creative storytelling, and for trying to take a famously optimistic franchise in a Darker and Edgier direction. Fittingly, the final battle pits the Enterprise against the Vengeance, the first Starfleet ship ever designed expressly for combat, and the ending has Kirk delivering a speech about the importance of Starfleet staying true to its original mission of peacekeeping and exploration.
The designs and whatnot for the Klingons were originally created for scenes cut out of the 2009 film.
Chris Pine recites the "Space, the final frontier" monologue before the end credits. For the 2009 film, Abrams considered having Chris Pine recite the monologue before letting Leonard Nimoy do it as a Passing the Torch moment.
The design of Earth's cities now has a very Mass Effect-like look and feel. From the vehicles, to the architecture, you'd half-expect to see a derelict Reaper near London. The Klingon ruins suggest a cross between Tuchanka and Ilos.
When Harrison takes out the Starfleet High Command early in the movie, it resembles the scene in The Godfather Part III.
Nibiru, the name of the planet in the opening scene, is the ancient Babylonian name for Jupiter (which has also been used in a couple of different pseudoscientific theories involving planetary catastrophes).
The room where the Starfleet captains confer and are eventually ambushed by Harrison looks very much like the archetypal war room seen in films like Dr. Strangelove and Fail-Safe.
Some fans were no doubt rolling their eyes when Abrams seems to setup a monster chase scene early in the film. The creature is instantly stunned and never seen again. Adding to the humour, it turned out that the monster was actually Kirk's ride, intended to help him escape from the horde of angry tribals pursuing him.
Ironic in that Star Trek II: The Wrath of Khan was originally planned to be entitled Star Trek II: Vengeance of Khan, because at the time the third "Star Wars" movie was announced to be 'Revenge of the Jedi.
Carol Marcus was supposed to be American like her original counterpart but was changed to English when Alice Eve was cast.