To ease any fears, I must say that the game's "fucked-up"ness stems mostly from gameplay concept, and not story. There are a lot oof odd, quirky things going on in the gameplay, like, for example, being able to heal by saving, turning the system off and waiting (a few weeks, depending on the injury).
And things like the game deleting your save if you mess with the internal clock.
I . . . really don't know how it does this. Just as I don't know how Boktai only works with real sunlight.
There are many, many more odd little weird things about the gameplay that I will not comment on, simply because I remember how great it was to play Metal Gear Solid 2 for the first time. The revelation of Raiden as the hero was perhaps the biggest shock ever in "cinematic" videogame history.
The question on everyone's mind is "Does Metal Gear Solid 3 shock on the same level as Metal Gear Solid 2?" I'll go ahead and answer, without spoiling anything, that no, it does not. There are a few huge, violent turnarounds in the story; however, Kojima knows (and he told me he knows) that he can't surprise people like he did with Raiden anymore. So rather than try to surprise with the story (which is a rather mature mix of 1's seriousness/preachiness and 2's flat-out mischeivous quirk), he surprises with the gameplay this time. He told me that's what he was going for, and . . . that much I understand now. So there are things regarding the gameplay that i will not spoil -- and I'm not talking about being able to hang from tree limbs with one hand and shoot guards on the ground with the other hand. You need to think slightly bigger than that. Think about LIFE and DEATH.
The idea of a game with a cliffhanger segment that required the player to access the internet at a specific URL and submit a certain piece of highly personal information (which would then be background-checked by Konami staff) in order to be granted a password to a game-serial-number-specific password to access the next part of the story, was something I presented to Kojima, causing him to explode into a really sick-looking smile. Though he doesn't do it in Metal Gear Solid 3, he's "thinking about it" for "something" "in the future".
In closing -- I think I know what Kojima's next game is!! He hasn't told me yet, though, well, I think I guessed already.
Anyway, as regards Metal Gear Solid 3 -- the US version is released on November 17th. That ain't too far away!! You will have it soon. So stop reading forums about it, because a couple of the pre-release (review) copies are going to be getting out soon, and that means people are going to start spoiling stuff.
SO!!! Go read a book! I recommend Kobo Abe's "The Woman in the Dunes," and so does Kojima.