Because it's convoluted, confusing and contradictory. I'm pretty sure that about 80% of the content in some of the games could be trimmed down and streamlined to be something a little more refined. The remaining 20% is stuff you've got to work out for yourself. And I'm not enthusiastic about the idea of Ground Zeroes being in the middle of the overall story - it suggests that Kojima thinks there is something more that needs to be said, which just shows how flimsy the overall storytelling is. Which is unfortuante, because the basic storyline for the entire series is actually pretty good.
I think Kojima's problem is that he is very verbose and not particularly articulate. Which is to say that he takes too long explaining things, and some of his explanations are very clumsy. After all, there were large sections of Guns of the Patriots where the player didn't actually do anything but watch extended cut-scenes.
Funnily enough, the best analogy I can draw here is to William Shakespeare, specifically Romeo and Juliet. It's his most popular play, but it's not particularly well-written. As I tell my students, Romeo in particular tends to say twenty words when two will do. Kojima does the same thing, and some of his dialogue is very heavy-handed.