MGS3 is a fantastic espionage-thriller with an engaging prequel plot, even if it does retain some of MGS2's flaws.
At the simplest level, I really enjoyed both playing and watching this game. The environments are stunning. This truth is most obvious in a prolonged sniper battle that makes the two in MGS1 feel childish by comparison. I have never paid this close attention to the audio-visual minutae present in a game before--never have they been so integral to the gameplay. The absence of the strictly defined fields of vision present on the radar screens made sneaking an organic experience rather than a simple stay-out-of-the-yellow-cone-and-don't-make-too-much-noise exercise. The sheer amount of time I spent crawling through the grass waiting for the opportunity to either evade or dispatch enemy soldiers made the codename "Snake" profoundly appropriate for the first time. And although the survival aspects were neither perfectly conceived nor executed, something about alternatively eating fresh cobra and prying bullets from your forehead with a combat knife made jungle espionage come across in a deeply visceral way. I have qualms with the story and the comic-book style villains (save the intriguing young Ocelot and the mysterious Boss). My sensibilities as a student of history keep kicking in--Kojima seems to want to evoke some kind of pseudo-intellectual cool by noting that his story/stories won't be found in history books. There is a difference between crafting human dramas and intrigues that fall underneath the radar of general society and throwing together crackpot consipiracy theories with outlandish characters that only retain a tenuous connection to real life. To both its credit and derision, "Snake Eater" has some of both.
I am forgiving, however, not least because I was once a Metal Gear Solid fanboy and "Sons of Liberty" never fully changed that, but also because after completing "Snake Eater"'s satisfying and surprising (though I should have seen it coming) conclusion I feel like I have more of an understanding of the observations about the world that Kojima is expressing through the character of Snake and his main rivals. Kojima's soldiers are pawns--part of a system far greater and sinister than they possess the power to resist. Snake, the Boss, Meryl, Roy Campbell, Big Boss, Raiden, Liquid, Ocelot and the rest are tragic heroes in a global drama of nation states and military-industrial complexes where the modus operandi is kill or be killed and the only certainty is death. Knowing this, I am able to understand the Patriots/Philosophers/La-Li-Lu-Le-Lo as the face(s) that Kojima wants to put on this evil system, as though maybe something that organized and destructive must have some kind of intelligent power driving it. I would be more satisfied, however, with a depicition of our geo-political nightmare as an evolving global ecosystem of peoples and technologies where the rules are not determined by a diabolical cabal but the ancient self-seeking principles of natural selection.