I never bought into the "the story is confusing and has to be discussed for hours, therefore is must be deep" perspective. Mice and Men is a deep story... and easy to follow. Being a good story teller, IMHO, inherently means being able to tell a story that people can follow. Let us say I am a professor and nobody in the class can understand me... are the students unintelligent and I'm simply brilliant or am I bad teacher?
Outside MGS1 and MGS3, Kojima's stories are a mess. He isn't a good story teller.