Fox did that to Naomi didn't he? The Storyline was so deep in MGS, I think it woulda done some good if they didn't make the MGS2 so much parallel to the first one.
They even tried justifying it at the end with the AI people were talking to him about the S3 concept. If they just went into the AI concept more or into raidens past i think the story woulda been fuckin amazing. Instead they decided to divide it 2 ways and make things eriely alike to MGS1...