I didn't understand 80% of the storyline the first time I played through it. It took me two or three playthroughs for me to somewhat grasp what the story was about, but even now, I'm not 100% sure. I am currently playing through it again for the first time in a long time, and now, I definitely understand why so many people feel the need to find reason and story where the isn't really any. I love the game, but lack of character development doesn't exactly help the already mediocre storyline.

A pea is green, regardless of how much I want it to be blue.