I don't know how I stumble into these things, but this website has a pretty amazing theory to explain the plot of Metal Gear Solid 2: Sons of Liberty. Of course, it's presented in an incredibly stupid format that feels like someone's html training experiment, but maybe that's part of the point. The article fully explains several ideas that came to my mind while playing (and plenty of other theories), but I did not have the research and reasoning behind me to put all these pieces together.
MGS2 was skewered by a major anti-plot backlash a year ago, which I always felt was just a typically disgruntled and jaded response to the incredible amount of hype that preceded the game's launch. I also feel it was mainly funded by stupid people. I personally thought that MGS2 had a fantastic plot, marred only by the over-reliance on codec text screens... screens that made sense from an in-game perspective but often became tedious to click through from a real life perspective.
The vast majority of gamers expect the plot to be handed over in a nice, Hollywood-style package. They want nothing more complex than the average action film. So a game that purposely throws out red herrings, conflicting information, psychological twists - and develops in a generally obtuse way - frustrates a lot of people. MGS2 wants you to think, in addition to all the action. The story is also largely confined to the limited view of one single character, meaning that there is no usual Narrator or Omnicient Voice directing the plot's presentation and explaining everything in an obvious fashion.
I guess it's too easy to assume that there is no explanation for the game's weirdness, that it's just poorly done. We're used to the idea that video games have no "higher meaning" and that underdeveloped, gaping hole plotlines are the norm. We're not used to a game that has as much to say as MGS2, but requires your mental participation to make sense of it all. To compound it all, your mental participation may not even be enough.
The thing is, I thought this direction was obvious while I was playing the game. I may not have understood it all first time through (and I still don't), but I instantly "got" that Hideo Kojima was telling an incomplete story, a story that was far more complex than my first-person character could understand. But I always read every single word and watch every single cutscene when I play, which I know many gamers don't bother to do. I even read the game's supplementary onscreen novellas. Reading is fundamental.
I found it extremely rewarding to play a game that was as difficult in plot as it was in action. I'm looking forward to the release of the extended edition, Metal Gear Solid 2: Substance. I'll make a prediction here that Substance will be a critic favorite, but flop in the common public. The game has a huge reputation problem by this point... even if you ignore most peoples' issues with the storyline, everyone is on the We Hate Raiden bandwagon. You can't even read any professional commentary on MGS2 these days without some obligatory line about the "non-gender whiny wimp" or similar. Plus, several newer games have risen that promise to be MGS2 "without all the stuff you hated about MGS2." That's fine marketing I suppose, but I don't see anyone writing webpages about the deeper meaning of Splinter Cell.
I'm not saying it's the most perfect video game ever either, by the way. I just like that it took a big risk, storytelling-wise.
If all you want is an action game, that's perfectly okay. Get Substance and turn off the cutscenes/dialogue. I think you're missing something pretty spectacular, but whatever. I just hate to see a great game get mishandled because most people choose to cut it off at the knees.