The game becomes more understandable if you ignore the anti-war aesop and consider it to only be anti-war videogames. The Mantel soldiers are the hordes of immature 18-34 young men who gobble up an endless flood of games where they mow down faceless hordes, Mantel itself represents the corporations who release games glorifying conflict and death, and Merino and his forces - the sketchily-drawn Excuse Plot bad guys? Well, no metaphor's perfect. This grossly oversimplifies things (for example, a large part of Halo's supposedly simple-minded plot is concerned with how the enemy of your enemy is not your friend), but that's roughly what you'd expect.
Merino could represent Indie companies that use innovation to gain market share before stagnating in the sequels. The rebels following him could be hipster gamers that still want to murder some dudes, but won't buy a title unless it discusses existentialism ad neauseum in the narrative. A good example would be the decline of the Painkiller series: rough round the edges but fun in the first game, declining rapidly into tedium with sequels and leading into Bulletstorm that is almost inseperable from the space marine shooters it attempts to parody.
In a sense it could also be a kind of parable about anti-videogame crusaders like Jack Thompson. The so-called rebels paint the entire Mantle corporation as some kind of corrupt shadow industry trying to turn the world into a wasteland...and yet at the same time they are just as dishonest and revealed to be just as corrupt, but (try to) excuse their actions by saying the "other side" is in fact guilty of worse. And like in real life, this is at least partially true, since even though it is entirely correct to say that it's simply not possible that the Mantle soldiers (players) are really horrible people and merely being manipulated, it does require you point out the COMPANY Mantle—not it's soldiers—is inherently corrupt and focused to the exclusion of all else on profit. So in the end, the player has to choose between two evils and try and figure out which is worse: censorship based on a dishonest claim, or resisting censorship only to pad the wallets of executives. At the end of the day the only victims really are the Mantle soldiers, and the Rebel soldiers, with the leaders on both sides being not-evil-but-still-douchey villains. And now I'm depressed.