If you have time to read essays on what video games are really about (congratulations, newly unemployed person and/or Cracked employee!), you'll learn that Kojima was making a statement about information control and the Internet. Specifically, he wanted to point out how easy it is to manipulate the willing by controlling the information they can access -- Raiden is manipulated by the villains of the game in the same way that fans were manipulated into thinking they were going to play a game they liked.
Now you know. And knowing is half the boredom.
There's much, much more to the whole thing, but to explain it all we'd need a 15-part analysis, a better grounding in postmodernism than Internet comedy has given us, and several bottles of grain alcohol. Long story short: Most fans missed the meta-commentary and were simply infuriated by the bait-and-switch, along with the confusing, fourth-wall breaking, and generally bonkers plot. Our hats are off to you: Truly, Kojima, you were the greatest gaming troll ever ... until Eve Online came out.