Part 2: War is Routine
PART 3: Snake Becomes Old
Obvious Reason
When "Old Snake" was first revealed in 2006, this was the general response. It was an odd choice, but people have become used to Kojima's "wackiness", so it seemed like par for the course to an outsider. Meanwhile, fans were just happy to have something new and exciting, and once again chose to overlook the less happy implications, even when Snake had a gun in his mouth.
The obvious reason for Snake looking like an old man is the fact that he was cloned, but there's more to his being "old" than simply having white hair and a moustache. His whole attitude is one of being tired and miserable, void of wit or grit, philosophy or care. And while it's true that in Shadow Moses he was reluctantly forced out of retirement in order to do his mission, it was a major theme throughout the game that he (not-so-secretly) loved the tension and conflict. No, this is a different kind of Snake, clearly at the end of his rope both mentally and physically. Is there a specific reason for this? More importantly, how does Snake go from his inspiring Philanthropy of Sons of Liberty to such a dejected, apathetic state?
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Think about it. The last time we saw Snake, he was part of a group called "Philanthropy" which was dedicated to eradicating Metal Gears and — evidently — spreading profound wisdom to future generations. They weren't naïve. They didn't see the world through rose-tinted glasses. They were motivated, resourceful, and damn good at what they did. So what the hell happened?
The truth is, no obvious reason is given for his decline in beliefs. We can assume that the change of war has destroyed his philosophical outlook, but considering the 180° difference, it's amazing that we don't have a clear discussion of how he became so... out of it. At what point along the way did he give up trying to fix the world? The official website says that Snake "disappeared after the Big Shell incident, but has now returned at the request of Campbell to terminate Liquid Ocelot." Huh. That's it? The Database says that his coughing fits and sudden aging forced him to abandon his plans to save Olga's child, but this is a weak excuse at best. Snake, who has always been "the man who made the impossible possible" is giving up on his ambitions and ideals because of coughing? Interestingly, the Database actually mentions that "OLD SNAKE" is what you get when you take the "IS" out of "SOLID SNAKE", clearly reinforcing the fact that he is lacking his essence.
The most widely believed reason for aging Snake was to ensure that he wouldn't be in any more games, which makes sense since Kojima wanted Snake to die or fade away, plain and simple. But this still doesn't account for the dejected personality. For that, we need to look at the hidden reasons.
The Hidden Reasons
It's hardly a "hidden" reason considering how vocal Kojima was about it, but Old Snake is a reflection of Hideo Kojima himself. He's apathetic because Kojima is apathetic; he's tired because Kojima is tired; he gave up on his philosophical idealism because Kojima gave up on his philosophical idealism (in regards 
to the Metal Gear series at least). Every major characteristic of Old Snake can be traced back to Kojima's own feelings about the series and his fans. The fact that Snake wants to get it all over with so he can die in peace is exactly parallel to Kojima's desire to end the series so he can move on without restrictions.
Snake is not supposed to be "cool" anymore. Those who think Kojima simply failed to make an enjoyable main character have it backwards: Old Snake is a success because he makes you wish he would retire already. He's not a hero or an anti-hero; he doesn't care about right or wrong anymore, he just feels obligated to clean up the mess he helped to create...
Snake: War has changed. Our time has ended. Our war is over. But there's one more thing I must do... One last punishment I must endure. Erase my genes... Wipe this meme from the face of the earth. This... Is my final mission.
There are many other aspects of Old Snake that combine to tell a story about Kojima's mentality. Take, for example, Snake's neutrality in the battlefield. Kojima emphasized early on that Snake would be sneaking through a warzone that he didn't care about; the whole "Side A versus Side B" scenario where you are a powerful but neutral factor is a possible reflection Kojima's disinterest towards the competing voices trying to influence him and the series. Hardcore fans, casual fans, his team, his bosses... Anything goes, as long as it gets the job done. The "OctoCamo" and disguises are akin to his battlefield neutrality, and serve as a metaphor as well. Kojima can't "hide"
from the questions or demands being made of him, so he is blending in and disguising to whatever is around him in order to get by. I can't help thinking this is why he allowed a total Westernization of the controls as well; justblend in and hope for the best.
Snake's sudden acceptance of knives and CQC is another example. When discussed with Otacon, this is what is said. There's no real answer given. Otacon is trying to understand repeatedly how he could refuse to employ such powerful techniques for so many years on principle, but then suddenly decide to use it now. But the best explanation is that Snake is instinctively reacting to the imitation CQC being used by soldiers around him; again, this demonstrates his willingness abandon his principles in order to overcome his obstacle. This isn't like Snake; certainly not the Snake of MGS2 at least.
Or how about the fact that Snake is suddenly slaughtering countless amounts of (quasi-) innocent women in battle? That's not like him either. The FROG soldiers and Beauty & Beast units were designed to demonstrate not only the extremely amoral state of war in the future, but Snake's willingness to stoop to it. Kojima doesn't go as far as to put child soldiers in the game for the player to kill, but endless amounts of brainwashed victim women is almost as gruesome.
Old Snake's "To let the world be" phrase is perhaps the most obvious betrayal of his former philosophy, as well as the most obvious hint about how Kojima felt about the way the series was headed. Letting the world be is the opposite of Philanthopy's motto, which was "Fight for your beliefs". This kind of drastic contradiction only makes sense in the context of Kojima's stark change in attitude over the years.
Of course, I don't believe that the Solid Snake we saw in MGS2 was intended to be the "real"
Snake, but rather a figment of Raiden's idealistic imagination of him (see The VR Theory), but this obviously isn't the official story, so the contradiction of attitude remains glaring and troubling from a story perspective. From a personal perspective the change is rather clever, since Kojima used Snake to tell his own story, but I'm sure this won't be appreciated by most fans.
Once we understand that Old Snake is a metaphor for Kojima, we can take his suffering and his apathy as a tribute to the tragedy of pressuring a creative genius. Without this symbolism, Snake's age and outlook in his final days are meaningless, and his part in the series is truly a depressing ordeal.
PART FOUR: Raiden is Cyborg Ninja
