Writer Walt Williams is not terribly keen on the game being described as an "anti-war" video game: he has stated that his primary intention was to create a narrative which asked players to question why they play shooters in the first place, and the War Is Hell aspect of the game came about largely as a necessary consequence of this rather than out of any special desire to attack war in its own right. The game grapples with how such a life and state of being would be one of constant fear, endless violence and bloodshed which would take a toll on any individual's sanity.
The game has often been interpreted as a critique of American military interventionism or at least the mentality of "good guys saving the world" that is used to justify such actions.
There's also one common thread running throughout Walker's various blunders in-game - every instance where things went pear-shaped because of his actions, it happened when he acted with only partial information. The mortars? He didn't scout the area thoroughly enough to find the civilians. The aquarium? He didn't ask any hard questions about why the CIA was there, instead trusting that they were on the level. In other words the story is not about War Is Hell so much as the dangers of incompetent and self-destructive soldiers being given command on a key mission.
And the biggest miscommunication happened at the very beginning, when he and his group were fired upon by other US soldiers believing that Delta Squad was working with the CIA. Had either side simply tried talking to the other, the entirety of the game could have been averted.
Alternative Character Interpretation: Most of the major characters in the game. The subject of how sympathetic Walker is as a character is one of no small amount of debate - is he a Well-Intentioned Extremist who becomes a Fallen Hero out of a misguided desire to save the people of Dubai, or a pathetic, selfish Heroic Wannabe who only cares about improving his own stature, regardless of the consequences? (The two are not necessarily mutually exclusive.) How much of Walker represents the player, and how complicit is the player in what Walker's done? Are Konrad and the 33rd really doing the right thing by staying in Dubai, or are they just as misguided as Walker himself? Was Riggs right to destroy the city's water supply? Etcetera.
There's really three different Konrads. There's the Konrad that Walker thought he knew, the hero who would never let the 33rd do all this stuff in Dubai. There's the Konrad that he thinks he's confronting later, the maniac he blames for everything. And then there's the actual Konrad, who seems like was once a decent man before everything spun out of control. The exact measure of the "real" Konrad is up for debate... just how much of a monster he was.
Angst? What Angst?: After the white phosphorus incident, Adams is clearly disturbed and Lugo begins freaking out. Walker, on the other hand, has no outward reaction, which flabbergasts Adams. Key word being "outward": the guilt of it drives him to insanity and causes him to start hallucinating. And given Walker's position in the chain-of-command, this also makes sense. Everything he said in that calm, cold tone after the incident was completely accurate - if the group didn't move from their position, it would only be a matter of time before other forces converged on their position. Keeping on the move will also help him avoid reflecting on what he just did. Pragmatism at its most disturbing.
Anvilicious: Thoroughly and unrepentant about it. The New York Times specifically criticized the game for its lack of subtlety and borderline-gratuitous content.
Audience-Alienating Premise: The game was advertised as a fairly standard military shooter, though it is emphatically not one, because it would be impossible to come up with an appealing way to advertise what the game really is to the people it was intended for.
Broken Base: After the white phosphorus incident, there are exactly and only two opinions that people seem to have (reactions so polarized as to almost drag the entire game into Love it or Hate it territory):
You either believe that it's a masterfully executed Take That! against both the player and the shooter genre, where it forces you the player to look at the more realistic aspects of using a horrible, horrible weapon in the name of progression, with no cutaways or easy answers. In a word, it gives something that most paint-by-numbers modern military shooters don't have: consequences.
Critic Ben "Yahtzee" Croshaw seemed to fall into both camps at once: He "felt like shit" for his initial delight at the white phosphorus "mini-game", but at the same time compared much of the game's horror to a person mooning you then criticizing you for looking at their butt. He did still make it his Game of the Year.
Cliché Storm: The gameplay is oft-criticized as doing everything that has already been done before in a third-person, military-focused tactical shooter without doing it in any remarkable way. The plot, however, is is anything but.
In an interesting way, Walker could be seen as a much darker take on Cloud Strife from Final Fantasy VII. Both characters desperately want to be heroes, but after committing and experiencing horrific acts, both lose their minds and make up a fantasy in their heads where they are heroes, as that is the only way they can cope with the trauma they received.
He can also been seen as a comparison to Sayaka Miki as characters who want desperately to be heroes, but find that they can't reconcile their fantasies with reality. Both resort to increasingly disturbing violence against what they perceive to be "evil", become consumed in madness, realise it far too late to undo what they'd done, and become warped, monstrous versions of the good people they used to be. Walker can also be compared to another character from a work of Gen Urobuchi, Kiritsugu Emiya.
Walker can also be compared to other Nolan North characters, especially Nathan Drake whose violent mowing down of countless mooks in his quest for adventure has raised many eyebrows for the fact that Drake seems indifferent and unaffected by the consequences of his actions. North's Walker shows the unattractive and darker side of such a standard character archetype.
Walker also exhibits some interesting similarities with Alden Pyle from The Quiet American and it's 2002 movie adaptation. Both characters are intelligent, well-meaning and seemingly idealistic Americans, but are self-deluding and destructive about their military intervention in a foreign country, denying the true evil they are complicit in and dissociating their actions from its consequences, and refuse to accept that they are truly the villains of their story. The most obvious difference between them, however, is that Pyle dies unrepentant in The Quiet American, whereas Walker comes to some understanding in Spec Ops.
Critical Dissonance: Critics, by and large, were impressed with the game's story and themes (if generally finding the gameplay decidedly lacklustre - neither noticeably good nor bad), but it sold very poorly. Players who did pick up the game were divided - one camp thinks it's brilliant for opening questions that many other games conspicuously fail to acknowledge about simulated violence, power fantasies, morality, and other assumptions that come part and parcel with the genre, in the frame of an affecting and stark character study - enough that a critical examination supportive of the game was written. A second finds it pretentious, hypocritical, self-righteous about imaginary violence, and too flawed in itself to be making any criticisms (especially in relation to criticism leveled at violence of the player, while being violent itself like the White Phosphorus incident). It was enough to spawn two games mocking Spec Ops' morality play: Video Game Morality Play and You Were Hallucinating The Whole Time. A third camp didn't care about the story and dismissed it as yet another shooter set in the tired modern military genre, with mediocre cover-based gameplay.
Cry for the Devil: The game welcomes you to empathize with Walker himself, and ultimately lets you decide whether or not he's redeemable.
Cult Classic: Predicted by writer Walt Williams, who noted in an interview that the game's Audience-Alienating Premise meant it was unlikely to ever be the sort of game with mass appeal. It has a hardcore following amongst certain gamers - usually those who seethe at the current trend of modern military shooters - enough to have a book written on it. At the end of the 7th Console generation, the game has become acknowledged as a classic of that era.
Darkness-Induced Audience Apathy: One might quite legitimately have this reaction to the game. By the end of the game, no one involved in the narrative experience of the game - not even the player - could be described as "sympathetic". Some marginally more sympathetic than others, maybe, but...
Death of the Author: Actually encouraged by lead writer Walt Williams - he noted in an interview that while he believes that the entire game is Walker's Dying Dream or "purgatory", the game is purposefully left open to interpretation.
Do Not Do This Cool Thing: Naturally, being a shooter with an anti-war message. For better or for worse, it is much more successful than most.
Enjoy the Story, Skip the Game: As is probably evident from This Very Wiki, the reaction among virtually all players and critics to the game amounted to "great story; bland, mediocre, repetitive gameplay" (with the exception of those players and critics who didn't like the story much either). It's no accident that the multiplayer mode, which features no narrative elements whatsoever (and wasn't even designed by the development team behind the single-player mode, who hated the Executive Meddling addition), is the single worst-received part of the game.
Escapist Character: This game, like Metal Gear Solid 2: Sons of Liberty, deconstructs the concept of escapism. You first start the game as generic, American soldier, Captain Walker; who is brave, fearless, and shoots first before asking questions. His main goal to saving hostages later turns into a sad, horrid Protagonist Journey to Villain plot. Because of Walker wanting to be the hero of his own story, he ends up killing his teammates and dooming the city of Dubai, along with all the civilians. Later on the game starts drawing comparisons between the player and Walker. Players who play modern military shooters as Power Fantasies.
Konrad:The truth is, Walker, is that you're here because you wanted to feel like something you're not: a hero.
Soldier: You know, Captain, we drove through this whole city to find you. We... we saw things. If you don't mind me asking, what was it like? How did you survive all this?
Walker: Who said I did?
From the dev's point of view, it was too effective at deceiving everyone; lots of players judged the game on the merits they would judge a typical war shooter, while the sort of gamer who would value it's dark plot and innovative narrative style would be turned off by it looking just like every other shooter following the leader.
Some of the graffiti in Dubai says "Under the sand, the pavement," which is an inversion of famous graffiti that appeared in France during the May 1968 protests, "Sous les pavés, la plage," or "Under the pavement, the beach" where it was used as a phrase of rebellion to indicate escape from regimented life.
The loading screens feature two unattributed Jean-Paul Sartre quotes, one of them paraphrased.
Konrad's quote "Everything is teetering on the edge of everything" is a Shout-Out to poet Charles Simic, which lead writer Walt Williams included with the intent of establishing Konrad as a Wicked Cultured character. The reference was so obscure that numerous players believed it was original to the game.
The site of Delta's white phosphorous attack on the 33rd contains a fountain of children holding hands in a circle. This is likely a reference to the Barmaley Fountain in Volgograd which becomes famous in a 1942 photograph juxtaposing the image of children at play with the destruction caused by the war on the city, then called Stalingrad.
Hype Backlash: A number of critics and players feel that the game's deconstruction and story aren't as clever, well-done, and mind-blowing as the game's fandom has claimed it to be, especially critical of the White Phosphorus and player-criticism aspects.
Inferred Holocaust: Amazingly for such a dark game, this trope ends up being inverted in a majority of the endings. The loading screens would imply that it rains after Walker and Konrad's "confrontation". Given the water supply being destroyed by Walker's actions, this would at least give the people of Dubai a bit of a chance to survive by the time reinforcements actually show up. There are, however, several strong suggestions that most or all of the game's endings are hallucinations or otherwise not real.
It's Short, so It Sucks: One common reviewer complaint is that this game has a full triple-A price, yet the campaign only lasts less than 3 hours (on easier difficulties). In comparison, even your basic Modern Warfare or Medal of Honor campaign usually lasts at least 5-6 hours for an average player. On harder difficulties, however, the average player will take about the same amount of time as that.
It Was His Sled: It's become fairly common knowledge that using the white phosphorus mortar inadvertently kills a large group of civilians, and the player character isn't the rugged, noble, mentally-balanced hero you'd expect him to be, along with the game's anti-violence spiels in the form of Konrad and the mocking loading screens that verbally berate the player.
Jerkass Woobie: By the end of the game, everyone. Even the player themselves.
Word of God says they wished achievements had not been included in the game for this very reason. Unsurprisingly, several reviews have criticized exactly this aspect of the game.
Several critics found that some of the more self-aware, Breaking the Fourth Wall elements of the game (such as Walker lampshading the use of In Medias Res in the helicopter sequence) took them out of the experience somewhat.
Under some of the loading screens is text such as "Do you feel like a hero yet?" or "To kill for yourself is murder. To kill for your government is heroic. To kill for entertainment is harmless." When you get more and more of these messages, some being repeated multiple times, eventually having no subtlety and saying things like "This is all your fault", it stops giving you a somewhat subtle feeling of guilt, and makes it feel as though the Radioman is now mocking you for playing this game. It doesn't help that the text occasionally breaks the fourth wall.
Love it or Hate it: There's very little middle ground between "a deep examination and necessary condemnation of violent games, violence in media, and player involvement" and "shallow, hypocritical, moralizing piece of garbage that insults players for taking the only path offered by the game". The middle ground sees the game as being an immersive dramatic work that is about experiencing a darker side of human nature rather than a simple putdown of the genre.
Misaimed Fandom: The game has a following among fans of classic/non-military shooters, who adore it for ripping the modern military shooter (and their players) to shreds. The game has an anti-violence message in general that applies beyond Call of Duty and its ilk.
Many commentators and fans have pointed to Yager Development's being based in Germany as a reason for the game's themes and message, arguing that such a profoundly subversive, anti-American game could not possibly have been made by an American studio. While Yager is based in Germany and has a multi-national staff, the game's writers and lead designer are all American.
As noted elsewhere, the game has received a lot of flak for its mediocre multiplayer component. Yager was not responsible for this aspect of the game (and indeed had no desire to include a multiplayer component at all); it was developed by a separate studio and included at publisher's insistence, or the game wouldn't have been approved.
Some gamers find it hypocritical for the game to call out the player for wanting to be the hero in modern military shooters while ignoring the developers' contributions by producing such games. However, the developers' responsibility is acknowledged in game with Konrad's suicide, a point which writer Walt Williams notes wasn't picked up on by the vast majority. 
If that doesn't count, there's also the ending where he slaughters the unambiguously friendly soldiers sent to pick him up (an entirely deliberate act, unlike the white phosphorus incident, which could be rationalized to some degree as accidental). Very much not coincidentally, it's something the player will have to consciously choose to do.
A lot of critics praised Spec Ops: The Line for deconstructing the modern military shooter (and the violence in games as a whole), but it is not the first game to do so - or even the first game in the last decade. Haze attempted it earlier, in 2008, as a deconstruction of game violence as a whole (the plot was sci-fi to attack the sci-fi FPSes of the time, but at one point, the game was to be set in Afghanistan as a modern shooter). Unlike The Line, however, it received mixed reviews for its controls, glitches, rushed development, and absurd story that removed many features and storylines and even less subtlety than in The Line.
Blacksite: Area 51 was also a similarly anvilicious, deconstructionist take on the modern military-themed/sci-fi shooter, but suffered the same problems as Haze. The game itself dealt with US foreign policy and has a similar You Bastard undertone.
Bizarrely enough, the game that helped start the trend of Take Cover! (that Spec Ops uses as a framework), kill.switch, had a You Bastard undertone and explored player agency. The player character was a faceless man working for a weapons corporation that profited by sending remotely controlled soldiers to start civil wars, and then selling weapons to both sides. You control one such soldier. It's further highlighted by the player character's callous dialogue and eventual death by a third party, who gives the soldier the PC had been controlling free will... and a chance to end the corporation that had been controlling him.
There were also plenty of jabs at games in general in Metal Gear Solid 2: Sons of Liberty; the player is led to expect they'll be playing as the previous game's beloved hero, and then finds they won't be; the player character seems to be an audience stand-in who reacts as the player would, but he's not, he's psychologically traumatized, regretful of his actions if he shoots a guard, and is supposedly trained on virtual reality (read: video games); the player is led to expect a standard power fantasy, then finds that much of the plot is dedicated to proving how little power/free will a player actually has; the player trusts the game, only to encounter Interface Screw, Fission Mailed, and other cracks in the fourth wall, all ending in the main character metaphorically shucking off the player's control. The main difference is that Spec Ops: The Line is more focused in genre criticism and less experimental.
Player Punch: The white phosphorus incident. The devs claim several people in their focus groups had to stop playing after that. Exactly as intended. Let's put it this way: it was so horrible, nightmarish, and downright realistic, that even someone as cynical as Yahtzee wouldn't dare to make light of the scene.
Rewatch Bonus: Lots of the foreshadowing becomes more apparent with added context.
The significance of Konrad putting his pistol in his holster in the opening cutscene is much more obvious in retrospect.
The Radioman can easily provoke a reaction in Adam and Lugo, but only Walker acknowledges Konrad.
Konrad's face seems to appear on an odd number of billboards, hinting that Walker is imagining him to be more important in their situation than he really is.
Scapegoat Creator: In this case it's a studio rather an individual. As noted elsewhere, the game was repeatedly criticized for its poor multiplayer component, but this element was not developed by Yager and they had no desire to include multiplayer in the first place.
Sequel Displacement: Most gamers probably aren't aware that there was an actual series beforehand, though the game is rather different from them anyway.
Signature Scene: The white phosphorus incident is pretty much the defining moment of the game, mainly because of being a massive Player Punch and the moment where the Genre Shift really kicks in.
Slow-Paced Beginning: The early parts of the game (presumably intentionally) seem like a generic, somewhat unpolished, modern military shooter. As it progresses, the story begins to play with and subvert the expected tropes, creating a more engaging experience.
Some Anvils Need to Be Dropped: The game has the Aesop of "war ishorrible", as do a lot of First-Person Shooter games, but it goes deeper than just that. The game goes on length about how everyone suffers in war and there are no true heroes in war, there is only death, destruction, and trauma awaiting for anyone who engages in war or is a witness to war. This game goes the extra mile and says there is no justifiable part of war, even if you're on the so-called good side, and we should not cross the proverbial line regardless of intentions.
The other major aesop that the game tries to get across is that of personal choice. You should never try to blame others for your own actions; you always have the option of stopping what you're doing and walking away from the situation. Short of someone pointing a gun at you and forcing you to do something, you always have a choice to do the right thing. It goes even further than that by reminding us that even if we have made a mistake, we still have the right to go home and do better next time; even in your failures, you have the choice to keep on living and face up to the consequences of your actions.
The game is equally unsubtle as a self-reflexive critique of the military-themed shooter genre itself. It argues that the genre more or less forces the player to become a Sociopathic Soldier with Black and White Insanity. Through its protagonist Cpt. Martin Walker, it demonstrates that acting like the protagonist of a shooter game in real life results not in victory but tragedy, and that such an individual would not emerge from the situation a dedicated, stoic hero, but rather an unhinged, maniacal, PTSD-ridden psychopath. All of this is demonstrated without an ounce of restraint.
It also makes a point about what happens to the people and objects around a shooter protagonist. Walker's desperate drive to be the hero ends up being the reason that everyone in Dubai will die of dehydration.
It also makes a fairly severe point about how the use of white phosphorous is horrific and devastating with several accurately depicted scenes of people being killed by it and the bodies left behind by it.
And that's not even getting started on how the game attacks the U.S. "foreign policy" of military intervention.
Actually, let's — the military brass explicitly ordered Konrad to get the hell out of Dubai before the storm hit, but Konrad (and the Damned 33rd) opted to stay to act both as a stabilizing element and in the hopes of organizing a mass evacuation for those that hadn't already gotten out of the city. Konrad himself was a Well-Intentioned Extremist at worst (as even the draconian water-rationing had a purpose), and his initial attitude was Screw the Rules, I'm Doing What's Right! when told not to intercede. However, this also reinforces the point that, regardless of how noble your intentions going in might be, things are not guaranteed to work out well in the end.
And on the other side of the aisle, the entire mess starts because those embroiled in Dubai's civil war believed that the trio of newcomers were members of those they were fighting, shooting on-sight rather than making any effort to assess their intentions.
Writer Walt Williams is not terribly keen on the game being described as an "anti-war" video game: he has stated that his primary intention was to create a narrative which asked players to question why they play shooters in the first place, and the War Is Hell aspect of the game came about largely as a necessary consequence of this rather than out of any special desire to attack war in its own right.
Another thing the game brutally deconstructs is the very purpose of the Big Bad itself. Throughout the game, Walker uses Konrad to justify his actions, since he needs to liberate Dubai from his martial law. However, finding out that Konrad was just a figment of his imagination Walker created to deny his actions not only deals a potentially Driven to Suicide reaction from Walker, but also is the straw that breaks the player's morale as well. Really, the deconstruction of a villain as a justification for the protagonist's actions applies to all forms of narrative fiction.
Spiritual Adaptation: Is a good one for Shutter Island book and film, both are about a protagonist with a pathological need of a heroic narrative to cope with their growing insanity, and post-traumatic stress.
That One Boss: That Heavy Trooper with the strobe light and the ability to teleport. Walker is hallucinating, but in most other cases, "dying" at the hands of a hallucination will just lead to a reload from the last checkpoint and the hallucinatory element vanishing. Not this guy. He'll kill you over and over again until he stops being atmospheric and starts being frustrating.
Play Chapter 6 on FUBAR difficultly. You have no backup, all your guns are gone, you are surrounded by enemy soldiers who can and will flank you any time you are not looking, and three shots from any gun kills you stone dead.
Chapter 14, in particular, expects you to push uphill to a guardhouse despite being up against two entrenched turrets. And while Adams himself says that "charging head-on is suicide", that's more or less what the game forces you to do against one of the bunkers…at very close range, with little cover, while well-armored, grenade-throwing enemies vault over the sandbags and melee you. You don't have many options other than bum-rushing the bunker and hoping you last long enough for Adams to help you take it.
Chapter 13: "Adams", on any difficulty. That is all.
A turret section about a third of the way through the game makes you Hold the Line while seemingly at least a platoon of American soldiers come at you. And they have RPG's, which can instantly kill you on any difficulty level. And there enough guys appearing all around your screen for you to keep them at bay.
The radio tower level is a pain from start to finish. It begins with a prolonged sniper battle where you are heavily outnumbered and all your cover is destructable. After you storm the place, you have to leave the way you came, right through a fresh helicopter full of Elite Mooks and fresh troops. Then you use the helicopter's mounted gun to cover one of your teammates as he makes his way to you. Then you have to defend the helicopter as you make a victory lap and destroy the radio tower.
Pretty much the entire remainder of the game after the helicopter crash. While Spec Ops was never generous with ammunition before, here it really gets strict and starts only allotting ammunition in quantities normally reserved for post-apocalyptic Survival Horror games like Metro 2033. The entire rest of the game is nothing but a Drought Level of Doom. Oh, and upon waking after the crash, you have only a handgun with 20 rounds of ammunition. And you are immediately beset upon by a dozen soldiers. You can kill them for more weapons, but they themselves hardly have any ammunition unless you execute them, which is very hard to do with how many enemies the game throws at you at once. And you are going to face more of them than ever before.
The yacht section combines all these problems with being attacked from every angle, enemies throwing grenades in confined spaces, and then having to deal with a frigging SANDSTORM.
The enemy's Last Stand is suitably brutal. You are just two guys on foot with nothing but personal small arms and grenades trying to attach a fortified position on foot, going uphill. Every single shot counts. It can take an hour to gradually grind your way up through the damn thing. And afterwards, you have to fight the toughest heavy in the game at very short range while he has a fully automatic shotgun.
Fighting to the final objective is difficult. Try as you might, you're pretty much going to have to change guns on just about every single fight as you deplete their scarce ammunition. And the resident tough guys are at their most plentiful.