The difference between nitpicking and deconstructing a movie’s flaws, I’m discovering, is precisely how they undermine the film’s own rules, or in the case of Star Trek Into Darkness, those created within the franchise as a whole. And thanks to J.J. Abrams’ “mystery box” approach to moviemaking, which builds feverish anticipation without much regard for how effectively that anticipation is paid off, he quite honestly invites the excruciating attention to detail that the film’s detractors apply to its internal logic, its loyalty to canon, and so on. An anachronistic coffee mug accidentally left in a shot of some futuristic location is mostly unimportant; razing the philosophical fundamentals of almost 50 years of sci-fi mythology in order to make a movie “exciting” for modern audiences feels, to this Trek fan, anyway, like a transgression of greater significance.

In terms of my Trek bona fides, I was not a big fan of the series as a kid, although I saw several of the TOS films in theaters, and really only came to appreciate the franchise’s complexity in the last five or 10 years. I was also a huge fan of J.J Abrams’ Star Trek, and although I dutifully reported on the sequel’s various developments over the last four years, I was mostly content to go into the follow-up open-minded, and with enthusiasm born from genuine affection for the 2009 reboot. But my frustration about and dislike for Star Trek Into Darkness has intensified, less because of some sense of personal outrage or a feeling of betrayal as a fan who felt “owed” something, than because it mostly undermines every concept that gave it the potential to be as great or greater than its predecessor.

As such, the following is meant to be a well-intentioned observation and analysis of many of the choices the film made, contextualized both in what the film’s aims seem to be with its story, and then within the larger context of the Star Trek universe.

The Prime Directive

The purpose of the Prime Directive is to preserve alien cultures by imposing an inviolable rule of noninterference – that is, members of Starfleet are not allowed to make themselves know to alien cultures because they might affect their cultural or technological evolution. This is literally the single most important rule in the history of Star Trek. But when Kirk and Spock (and later, Kirk and Admiral Pike) argue over the moral implications of violating it in order to save Spock’s life, they are all forgetting that they have already violated it, even before the aliens saw the Enterprise, by trying to save the aliens with a “cold fusion” bomb.

Pike points this out when he’s chastising Kirk, but it seems virtually impossible that a thinker as logical as Spock couldn’t have realized that in “throwing Kirk under the bus” for violating the Prime Directive, he hadn’t already committed the same transgression himself. (Which is not to suggest that Spock shouldn’t have been honest in his report, but that he should have shared some of the culpability.)

Who Is Captain Kirk, and What Does He Need to Learn?

At the beginning of Star Trek Into Darkness Kirk has become an arrogant, self-important lothario, qualities which he attributes to the fact that not one crew member has died during his tenure as captain of the Enterprise, and that he can apparently get busy with two ladies at the same time. Admiral Pike informs him that he needs to learn the value of losing crewmen (and women) and develop some maturity, but fast.

Precisely how this manifests itself, and is later paid off, is painfully unclear; although Kirk certainly loses a large number of crewmen during Admiral Marcus’ attack on the Enterprise, he scarcely has time, much less reason within the film, to contemplate the loss of life, and his later sacrifice exists primarily to provide the film with a “Wrath of Khan” narrative parallel rather than evidence of any personal or professional growth.

As much as Pine’s interpretation of Kirk exists at perfect right angles to William Shatner’s (which is moderately maddening for a fan of TOS), the problem here is less canonical authenticity than thematic continuity. Sure, Pine’s Kirk is a young guy and he needs a heaping dose of humility – a fair problem for him to exorcise -- but how is an audience supposed to feel when he does not learn that? His renewed swagger at the end of the film – after he’s been brought back from the dead, possibly indicating he’s now literally incapable of dying – hardly indicates that he’s developed any greater appreciation for the value of life, much less that he takes his responsibilities as captain more seriously than a kid might if his parents gave him permission to take out the family’s “nice car” anytime he wants.

Spock’s “Illogical” Feelings

As Devin Faraci of Badass Digest pointed out, Zachary Quinto probably plays the best Vulcan (or at least one of the best) since Leonard Nimoy himself, and his performance consistently nails exactly the right tone of directness without descending into disdain or condescension. But his evolution in Star Trek Into Darkness is, to put it mildly, not logical.

In the opening scene of the film, Spock resigns himself to death on Planet Nibiru after assuming that Kirk will uphold the Prime Directive and leave without him (or at least not rescue him). When Kirk saves him anyway, he’s less appreciative than nonplussed why his Captain would break the rules on his behalf. Meanwhile, his lady friend Uhura is upset that he seems indifferent to his own death, not to mention her grief at the prospect of him getting burnt up inside an alien volcano. This leads to a scene in which Spock confesses that he does indeed have feelings, but he holds them back so that he won’t revisit the pain he felt when his mother and his home world perished during the events in 2009 Star Trek.

This is all fine, one supposes, but then what the fresh hell happens to Spock at the end of the film? After skillfully outwitting Khan/ John Harrison, he rushes down to engineering to find that Kirk has sacrificed himself in order to save the ship, and the audience is subjected to a fairly excruciating retread of the end of Wrath of Khan. And while I can understand that Spock would indeed have feelings for Kirk, I find it generally preposterous that a man – even a Vulcan – who watched his entire home planet go up in flames could maintain his resolve through that experience, but lose his composure after a guy he’s known for a year, and who quite frankly he seemed to argue with more often than agree, dies. Even then, it’s understandable if Spock capitulated to his feelings and dispensed a salty tear, but the film shamelessly punctuates the moment with a mostly phony burst of outrage in which Spock bellows Kirk’s iconic “Khaaann!”

The Khan Problem

It’s easy to assume that critics and journalists dislike J.J. Abrams’ “Mystery Box” approach because it deprives them of scoops or otherwise violates their efforts to uncover every secret in his movies. But the reason it backfires in Star Trek Into Darkness is the same reason it worked like gangbusters in Iron Man 3: because Abrams insisted that there were spectacular surprises in the first place. By placing Mandarin front and center in the ads for IM3, audience expectations were clear – they would be watching the eponymous hero fight one of his greatest adversaries, and they could thrill at precisely how Shane Black and Marvel updated him for the silver screen. And it’s not the choice itself, but the deliberation and subterfuge surrounding John Harrison/Khan which undermines its actual impact once viewers know the character’s identity. “Oh, so it was him all along, huh? Cool, I guess.”

Revealing early in the creative process that Harrison was Khan – or just calling him Khan from the get-go – could in fact have killed two birds with one stone. First, it could have quelled a lot of journalistic speculation that may inadvertently led to other secrets being divulged, and encouraged the press simply to look forward to how he was treated, given Abrams’ terrific handling of the characters in Star Trek. But given the pretense that Abrams seems interested in making these movies for non-Trek fans, it could have provided those selfsame nonfans with a foundation or context for their entry into the sequel. And the reason why that is or might be important is because the surprise only matters if you know who Khan is already. If you’re not a longtime fan of Star Trek, the name Khan is meaningless – as meaningless as John Harrison – so by the time his “true” identity is revealed, it doesn’t matter. He’s already this movie’s villain, simply with another name.

Is This a Different Trek Universe, or Isn’t It?

Using Leonard Nimoy in Star Trek was a mostly brilliant move, because it established that the original series and the TOS film all existed, but Abrams had the freedom to create and reinvent and basically do whatever the hell he wanted with the franchise since his was specifically distinguished from its predecessors. And indeed, creating a Khan for the Abrams universe was his prerogative – and there’s no major reason to object to that choice with the understanding that (aside from the actors) Ricardo Montalban and Benedict Cumberbatch are different people.

So why, then, bring back “old Spock” again to confirm, in spite of the character’s own admitted reservations about disclosing too much information about his timeline, that this Khan is the same one? Notwithstanding the fact that the conversation between “new” and “old” Spock begs for more context and substance than a two-minute scene, that exchange of dialogue undermines the entire idea that Abrams is operating with the understanding that what he does is separate, unique and most of all different. Then, of course, there’s also the fact that this conversation between the Spocks occurs on the bridge of the Enterprise in full view of at least a dozen members of the crew – and if that’s alright, was there a time when someone at Starfleet decided to reveal the existence of two timelines, and so on, to all of its enlisted men and women?

The Poor, Poor Klingons

If the Klingons are Starfleet’s most formidable opponents in the galaxy, you wouldn’t know it from Star Trek Into Darkness. Their appearance in the film is cursory at best, spectacularly dismissive at worst. Independent of Abrams’ pointless reinvention of their look, he employs them as identity-less cardboard villains who pose an ambiguous threat and are killed before they demonstrate any personality whatsoever. And the bigger irony is that they are still more or less poised to be Starfleet’s biggest threat, not only via the way they’re introduced in Star Trek Into Darkness, but certainly after a rogue Starfleet admiral sends Kirk on an unsanctioned mission to their homeworld, whereupon arriving he and his team (even if John Harrison does most of the work) kill a random Klingon patrol, which even the admiral acknowledges will be perceived as an outright declaration of war.

(Suffice it to say that Abrams was quite possibly setting up the Klingons to be the main adversary in Star Trek 3, and that’s fine. But at this point, they are no more distinctive than any other alien race, and quite frankly, not worthy of the distinction of being Starfleet’s greatest enemy.)

Dammit, Jim, I’m a Doctor – but Not a Very Good One

When did several members of the Enterprise crew become incompetent at their jobs? The characterizations of Bones, Scotty and Chekov in Star Trek were brilliant in that they captured the essence of the personalities of the actors who previously played them, while giving the contemporary actors a real sense of ownership of them within Abrams’ new universe. But in Star Trek Into Darknes they’re scarcely capable of completing the most basic responsibilities of their respective positions aboard the Enterprise, much less showing the sort of next-level intelligence and critical-thinking skills that made them standouts in any Trek universe.

Scotty, for example, can plainly recognize that Starfleet stole his transwarp design and used it to create a portable transwarp beaming device, but he can’t, say, figure out how it works. Or re-create it so that Kirk or someone else can pursue John Harrison on Vulcan without having to dispatch an entire ship, and therefore threaten a tenuous peace struck with the Klingons.

Bones, meanwhile, has 72 frozen specimens of superhuman biotechnology aboard the Enterprise with him, whose chemical makeup is confirmed to be the same as Khan’s. But after he decides to try and save Kirk’s life by pumping some of Khan’s blood into the captain’s corpse, he insists (1) that Spock has to go after only Khan to get that blood, and (2) keep him alive. It doesn’t take a medical degree to presume that the blood in those 72 other supermen is just as effective at regenerating life as Khan’s, or even if it wasn’t, that Khan, who’s now been confirmed as a diabolical tyrant, needs to survive a fight with Spock in order for them to use his blood.

Third, Chekov demonstrates in Star Trek that he can beam two people from a moving position – falling to their deaths -- onto the Enterprise, which is by any standard a remarkable feat. But in Into Darkness, he can’t beam Spock back onto the Enterprise without a line of sight (thanks to the heat of the volcano, I believe), and then later, twice, he can’t beam Khan onto the Enterprise from a moving location, even though he can beam people down directly to him. (All that said, he’s absolved of culpability for fouling up engineering – that isn’t and never was his job.)

And Then Nothing Bad Happened Ever Again

There’s probably another 1900 words that could be written about the incalculable emotional currency of Wrath of Khan Abrams and co. exploited for the climax of Star Trek Into Darkness, but instead it will have to suffice it for me to say that I’m mostly just grateful that they didn’t include the line “I have been – and always shall be – your friend,” even if they gave “Khan!” to the least likely character in Trek history to say. But the bigger problem with the end of Star Trek Into Darkness is how summarily it wraps up storylines that absolutely demand more nuance and intelligence.

So what exactly was Admiral Wallace’s plan again? According to the film, it was to thaw out Khan so that he would either help develop weapons against the Klingons, or fight the Klingons himself. When that plan backfired, Khan took revenge and then beamed himself to Kronos in order to figure out a way to rescue his frozen colleagues. Marcus then sent Kirk on a secret mission to obliterate Khan, armed with “experimental” photon torpedoes which he instructed Kirk to fire at Khan – an act of mean-spiritedness which, if successful, would likely be seen as a declaration of war against the Klingons. Simultaneously, Marcus commissioned the construction of a massive Starfleet warship, the Vengeance, of whose existence no one else at Starfleet was evidently aware (except its warmongering crew).

In short, he wanted to reunite Khan with his fellow superhuman soldiers, and then blow them all up while simultaneously starting an intergalactic war with a race that, in this timeline, has never demonstrated an imminent threat to Starfleet or the rest of the galaxy. And when none of that worked, Marcus would take the Vengeance on its maiden voyage, destroy the Enterprise, and falsify evidence that Kirk and his crew were treasonous. (We’re in a future that allows people to teleport billions of miles in seconds, but can’t master “little black box” technology on a spaceship?)

Meanwhile, Kirk is dead, but thanks to Khan’s blood, he’s alive. If the film had let audiences believe he was dead, but even revived him at the beginning of Star Trek 3, that would have been a more emotionally authentic payoff, especially given how much of the rest of the end of the film mimics Wrath of Khan, which more or less did the same. But the finale of Into Darkness cuts from the black of Spock knocking out Khan to Kirk waking up in a hospital bed. He is fine. Khan has been returned to his cryogenic pod, without any information about a trial, or God forbid a single sentence of the rationale for why he wasn’t simply executed (I choose to believe it was a feeble, too-late attempt to uphold Starfleet’s integrity).

Ultimately, Star Trek Into Darkness not only betrays the original Star Trek canon, but more critically it betrays the one that Abrams himself created with the 2009 film. Characters who were once incredibly gifted are now incompetent. The lexicon of Trek – phasers, transporters, warp drives – was jettisoned, undermined or otherwise ignored in order to make its set pieces more “exciting.” And its philosophical foundations were reduced to ash to provide moviegoers with something “fun” and visceral, even if those qualities needn’t be mutually exclusive from intelligence and complexity.

Certainly Abrams deserves to impose his own vision upon material he tackles, and he follows a long line of enormously creative people who have expanded the parameters of Trek with their stories. But the first time he made Gene Roddenberry’s world his own, he made something that was faithful to Star Trek as well. This time, he made it at Trek’s expense.

MORE: For an alternate take, read this: Our 'Trek' Expert on Why ' Star Trek Into Darkness' May Be Summer's Best Blockbuster