The story is complex, but that doesn't mean it doesn't make sense. For someone like me whose beaten each game of the franchise atleast three times(Metal Gear Solid 1 four times) it makes perfect sense. Kojima leaves things in mystery for a reason, such as the Lalelulelo and The Patriots, Olga's baby, Vamp's immortality... and he's always done that. Metal Gear Solid 2 in particular brought in a lot of philosophical and government-influenced concepts. In the beginning of Metal Gear Solid 2 we meet a character named Fortune who can't be harmed by bullets or any projectiles. The player is going "WHAT?! How unrealistic." and by the end, without spoiling it, you realize how and why. Metal Gear Solid is original, and realistic in it's own time. It's almost as if it doesn't take place on Earth, but a more imaginative and off-centered Earth. It's that japanese originality that gives it that 'feeling'.
It isn't like Splinter Cell in that it isn't a game that's sole purpose is depicting realism. Instead it draws from realism and is inspired from fantasy.
Kojima always seems to focus on Heroism and always brings in a set of interesting characters that usually harbor their own motives, have their own story and their own conclusion.
The game makes sense, it's just complicated (as is 'real life'). Mystery is a great element to work with, it draws you in. If everything was presented to you right away there wouldn't be much intrigue. Kojima has promised to tie all ends, and I can't even imagine what he has in mind, but I know it will be good.