Arrrrghh! Patriots do not = Philosophers!
Ok here goes, MPO. MG1, MG2, MGS1, MGS2, MGS3 spoilers and all!
The Philosophers is a secret organization made up of the United States, China and Russia during the Second World War. After WWII, the organization started to crumble, backstabbing itself, and working against one another. The organization that once gave hopes of a united world became nothing but a mere shell of its former self. The Philosophers now thrived through the creation of conflicts and war, this is how they maintained their power. We don't know what happened to the Russian and Chinese branch of The Philosophers, but we know that the US branch was actively seeking the funds of the organization (The Philosopher's Legacy) so they could take it all for themselves. In MGS3 they succeed at getting, supposedly, half of it, thanks to the works of The Boss, Ocelot, and indirectly Big Boss.
Ocelot is the son of The Boss. He was taken away from her by The Philosophers when she gave birth to him on the battlefield. The Philosophers had so called "charm schools", were they raised children for the organization (such as Eva, who was raised by the Chinese branch). He was raised as a US Philosopher Agent, often working as a double/triple agent. It is thanks to him, in part, that the US Philosophers got half of the legacy in MGS3.
We don't know if he was aware that his mother was The Boss, but it is likely considering the way they interact with one another (mainly during Big Boss' torture scene and his "plan" revealed at the end of MPO)
In MPO we find out that Ocelot has been working AGAINST The Philosophers for some time. He backstabs The Philosophers, takes the Legacy back, and claims that "It's all part of our plan to make the world she envisioned a reality!". We are supposed to believe that therefore he has been working with someone, or some people, to make the world The Boss envisioned a reality (her dream was to reunite the world, but by the time she had the power to do so in MGS3, she had become nothing but an empty shell, due to all the sacrifices she had made for her country, she no longer had a will to live, she had nothing but pain left inside her, and therefore passed the torch to Big Boss). We find at out that Ocelot has been working for a so called "mystery man" who is almost 100% certainly Major Zero. Now that they have The Philosophers' Legacy, they create a new organization to supplant them, one "true" to The Boss' vision: The Patriots.
Note that we have no idea if this is truly what The Patriots seek to do, but it is what Ocelot believes they stand for. MGS2 seems to point otherwise, but it is unclear what may have happened by then or what they are actually trying to do.
At the end of MPO, the mystery man asks Ocelot to help him with a project. This project is to analyze Big Boss' genetic make up and clone him: Les Enfants Terribles. Ocelot says he will help him with the project, but ON ONE CONDITION: That Big Boss joins them, so that together they may become the true Patriots. Ocelot has had a MAJOR obsession with Big Boss ever since he met him (or at least an obsession with his strength). It's unclear why, but ever since he has been part of projects related to Big Boss or his succession. Anyway we do NOT know if Big Boss accepts to join The Patriots or not. If he does, then Ocelot helps the mystery man with the LET project, if he doesn't then Ocelot does not take part of the LET project. My guess is Big Boss joins, and if so then it means Big Boss may have been part of the LET project willingly. We don't know why The Patriots wanted to create the Snake brothers, yet. Either way, we should believe that it remains part of their plan to make the world The Boss envisioned a reality.
One pattern that is important to recognize:
A "bloodline" (figuratively speaking here) has been attempting to reform the world order. The Boss, Gene (last boss of MPO), Big Boss, Liquid Snake and Solidus Snake. All of them in the end are successors to The Boss, some of them quite indirectly.
The Boss described The Philosophers she desired to reform as the following:
The Boss: The Philosophers of today have no sense of good or evil. Their influence extends to countries and organizations involved in every aspect of every war. They have become war itself. That's how they operate. The sacrifices of war cause a shift in the times. This shift leads to renewed conflict and in turn triggers the next war. Like a nuclear chain reaction, each conflict sparks countless others, forming an endless spiral of war that will continue on for eternity. Do you understand what I'm saying, "Snake?" By consuming me and you the Philosophers intend to keep their cycle going forever.
This is IMPORTANT!
In MPO, Gene (who describes himself as the true successor of The Boss), has the following goal:
Gene: I'll create a new global balance of power of my own design. My goal of building a new nation of mercenaries with only the most capable soldiers is real. But this peninsula is not the right place for it. Our nation will be an organization of shadows, without shape or form. We will lurk deep underground and intervene in conflicts all over the world. History will be ours to control. I will accomplish what the hollow shell of the Philosophers could not with a superior breed of soldier. This organization will be the true "peninsula of the dead". I call it "Army's Heaven." I will not allow the world to be a playground for abstract national interest and petty political gambits. I will use superior force of arms to achieve superior force of will. Thus I will make the world whole again. For I am the Successor, and this is my calling.
As you can see Gene's goal does not sound like what The Boss desired, it sounds like her description of The Philosophers. It's as if someone twisted The Boss' dream and created this false successor in an attempt to ruin it and at the same time prolong The Philosophers' rule under a different name.
Big Boss: You use fear to keep your soldiers in line. You use words to deceive your allies. You exploit those who look up to you as a mentor and then you throw them away! The country you're building is no heaven for soldiers. The place they're looking for is outside your "heaven." <--- Outer Heaven hint
Big Boss, who was the most beloved disciple of The Boss, and who was shaped by her to be the man he became at the end of MGS3, is clearly standing up for what she stood for, for her dream (she also stood against using soldiers as puppets, this is what she tells him and at the same time she forces him to kill her simply because it's part of the mission, she wants him feel what she felt when killing The Sorrow, she wants him to WALK AWAY FROM THE ROAD SHE WALKED). Gene on the other hand is standing up for something else entirely, and he eventually realizes this.
Now flash forward a few years to Metal Gear 1. Big Boss is supposedly now a bad guy, having created a nation fortress called Outer Heaven, and supposedly threatens the world with a bipedal tank capable of a lunching a nuke. This does NOT sound like Big Boss nor does it sound like he is making The Boss' dream come true. Either way, Solid Snake is sent to kill him. He succeeds at destroying Outer Heaven, but Big Boss survives.
In Metal Gear 2 Big Boss is back, and this time he created an uprising, known as the Zanzibar uprising. His goal? A continuation of what he was doing in Metal Gear 1, again nothing like The Boss' dream:
Big Boss: Once you've been on the battlefield, tasted the exhilaration, the tension... it all becomes part of you. Once you've awakened the warrior within... it never sleeps again. You crave even bigger tensions, ever bigger thrills. As a mercenary, I'd think you would have realized that by now. You care nothing for power, or money, or even sex. The only thing that satisfies your cravings... is WAR! All I've done is give you a place for it. I've given you a reason to live.
You saw those children, didn't you? Every one is a victim of a war somewhere of the world. And they'll make fine soldiers in the next war. Start a war, fan its flames, create victims... Then save them, train them... And feed them back onto the battlefield. It's a perfectly logical system. In this world of ours, conflict never ends. And neither does our purpose... our raison d'etre.
On the battlefield, you and I are valuable commodities. But back "home", we're nothing but dead weight. If we're lucky, we might get the attention of some two-bit journalist from a cheap tabloid. You and I are doomed to remain here until we die like dogs on the battlefield.
It doesn't matter who wins here. Our fight will continue. The loser will be liberated from the battlefield, and the survivor will live out the rest of his days as a soldier.
This sounds again nothing like The Boss' dream, nor even like Big Boss himself. It sounds more like Gene and The Philosophers. The part I bolded is exactly what The Boss told Big Boss about how The Philosophers had become. Either Big Boss got crazy in the head between MPO and MG1 (even tho he clearly put some sense into Gene and demonstrated he rejected him and The Philosophers' way). I doubt he strayed from The Boss' path, we just don't know why he is acting this way in MG2 (I wrote a lot about this on MGS:TUS but to put it shortly, in order to make sure that Solid Snake would be his successor and one that rejected the ways of The Philosophers, Gene, and whoever else planned to recreate such a world of war, he posed himself as madman and forced Snake to reject him, a bit like The Boss did to him in MGS3 when she pretended she had betrayed her country, but to make sure that Snake would reject him completely and hence be free and think for himself, he never told him the truth. Basically a father who didn't want his son to become like him gave him a beating and made his son hate him. Liquid on the other end obsessed over becoming like Big Boss (oooh so did Ocelot, hint hint Liquid-Ocelot), and even wanted to surpass him).
Solidus Snake, who is supposedly the perfect copy of Big Boss, or at least a balanced copy, was not as extreme in his actions. He wanted to bring back freedom to the US and free the country from The Patriots' rule, which by the time of MGS2 seem to have become no different than The Philosophers, Gene, or what Big Boss seemed to represent in MG2 (strange for an organization that supposedly stood AGAINST The Philosophers and wanted to make the world The Boss envisioned a reality).
Liquid Snake, according to Campbell's description of him and his plan in the 15 min trailer, appears to be doing exactly what Gene was doing (and there are already many parallels between him and Gene, especially in the new E3 trailer). So again we may believe that in the end EVERYONE except Solid Snake has been the true successor of The Boss.
As for Ocelot, I think he also is sort of a false successor. He's trying to make the world she envisioned a reality, but in ways that are incompatible with The Boss' way of thinking. In the end she did not chose him as her successor, she chose Big Boss, and Big Boss appears to have chosen Solid Snake. Ocelot believes in MGS2 that the S3 plan is to create a soldier on par with Solid Snake (hello! Obsession with Big Boss' strength again!), which is similar to the LET project he decided to be part of (again shows an obsession with Big Boss, at least his character of strength). And don't forget how he grafted Liquid's arm on himself, another sign that he is trying to "take" Big Boss' qualities for himself, to achieve his plan by force. But again showing that you can't make someone's dream come true if you don't live up to it to begin with.
That is that.
Phew (no one will read that!).