The story is poorly told, constantly repeated to make sure you got it, explained 600 different ways while Kojima was still deciding which versions to retcon out, and really at the end of the day wasn't all that special.
Gamers generally accept this because we're not used to stories taking place in games. Sure, we have "action movie" or "generic space opera" stories a fair amount, but it's rare to get anything more complex, so people fawn over MGS's storyline as the Sophie's Choice of our medium. The problem therein being, as already expressed, that Kojima had (at its bones) a relatively simple storyline going, but he's so bad at telling it that the complexity goes off the scale.
So no, I didn't care for it. You get the same "epic" moments in a bankrupt storyline game like Gears of War, with the added advantage of getting to spend most of the game playing the game. If you have to spend over seven hours explaining something that I could break down in twenty minutes, you're doing it wrong.
- J