Warning, this contains spoilers. I posted this in general off-topic, because this is more of a discussion about the philosophy behind the series
The Metal Gear games are my favorite form of anti-war art, as they have a great deal of depth to them. They replace the black-and-white morality that the media is rife with, and they place players in a situation where they end up killing the real heroes of the franchise. While arguments can be made for the morality of most antagonists in the series, I shall focus on Outer Heaven. By all means, feel free to point out other examples in the series, as there are plenty of them.
In the first Metal Gear game, the United States tries to topple the government of Outer Heaven and subvert their nuclear ambitions. While carrying out his mission, however, it quickly becomes apparent that the soldiers of Outer Heaven are the real heroes and that the United States isn't. Outer Heaven was formed to prevent soldiers from being manipulated by their governments and is a society that revolves entirely around the military.
If the noble goals and structure of Outer Heaven isn't enough, it becomes apparent in sequels that the American government was under the control of a group known as The Patriots. The Patriots were only using their soldiers as puppets and even killing their own people to cover up their operations against the Chinese/Russian Philosophers in their secret cold war. Outer Heaven was formed in response to NATO, Chinese and Russian governments taking advantage of their soldiers and was formed to protect soldiers from abuse. I don't know about you, but I think Outer Heaven were the real heroes of the Metal Gear universe. What do you think?