You read a lot of Tom Clancy novels, don't you? I love the Metal Gear series, but its storyline is completely nonsense, thematically hollow, and divorced from its gameplay, permanently. The reason that it takes place in an alternate history of the world is that every single theme or talking point Kojima wrote has been proved wrong, sometimes within the fabric of the game. Genetic engineering, the merits of pacifism (the Philosophers were who, again?), the fundamental corruption of national governments, nuclear deterrence, the lucrativeness of war? Kojima is clearly not paying attention to world affairs. How's it go, again? "War's no longer between nations, ethnicities, or ideologies"? Ooh, eerily prescient, Kojima! Too bad your ages-long development time caused Metal Gear Solid 4 to be released right in a massive worldwide resurgence of exactly that.
Er, no. That's "an economy," one where diversified sectors build products that people want and use their money to buy products from others doing the same thing. A "war economy," as Metal Gear Solid 4 says, is one where the vast bulk of the economy is used to fund a military state that crushes and absorbs other economies. No one's operating zaibatsu in 2008.
...I feel like you're not really grasping what Kojima is saying and how it is different from what you are saying.
It doesn't. Look at Shawn's questions in the comments section of N'Gail Croal's for-once-not-over-the-top article on Metal Gear Solid 4. The problem is that the fantasy undermines the obstensible themes. Tarkovsky's "Stalker" is a (kind of) science fiction story that doesn't.