There's nothing wrong with enjoying how Kojima presented the story, but please don't confuse it with good story-telling. It played out like an essay, as if someone wrote a paper on the history of MGS that was being read by different characters. Great works shouldn't have to rely on long-winded explanations to convey their messages. That's spoon-feeding information rather than letting your audience interpret meaning. This actually detracts from its intellectual value. I'm not saying it has to be intellectual to be enjoyed, but when you're discussing the philosophical merits of the game (like many people have been), it needs to be held to the same standards as any other art form.
It's unfortunate (for me, anyways) Kojima took this approach. I thought every other aspect of the game was great.