The story is just chronically stuip all around. Kojima doesn't do a very good job of painting the state of the world. Not that he does much better in previous games, but at least in those we can safely assume that the world of the games is basically identical/very similar to the real modern world. In MGS4, we're given the impression that the world has drastically changed, but we never really see that. To make things worse, the story has a global scale, rather than the small, isolated scales of previous games, where the actions of the story would be unknown to anyone that hadn't taken part in the story. MGS4 instead brings us a story of Ocelot trying to achieve world domination, and it just feels silly--even sillier than games have seen in the past. And unlike the previous game, Snake Eater, it doesn't appear to be paying homage to movies or anything, so it's kind of difficult to excuse the tone. Here, when the game goes over the top, it seems labored and stupid, rather than self-knowingly winking and silly.
Also, moreso than in previous games (except for 2) it felt like Kojima didn't really know when to stop when it came to cutscenes. They really go on for way too long, and more than once, I was saying to myself "why are characters saying so many lines that basically mean nothing? Is Kojima in love with the sound of their voices?" So many minutes and lines of cutscenes are wasted on a nonsensical, boring story (we've gone from nuclear explosions to zzzzz naughty computer AIs) told by characters that were never informed about the whole brevity being the soul of wit thing.
But whether or not you buy and don't but concerning the stupid/silly ratio of the story, here's the number one reason why the narrative is a failure: it's just not very good in comparison to previous games. Previous MGS games have always arisen in the neverending discussion about whether video games are art or not. If you think MGS4 is a great example, all around, of video gaming as a medium, and you think it is fit to be held alongside any piece of art anywhere, then video game forums probably are the only place you should be heard. lol.