@climhazard5: It was bittersweet for me. Ever since Peacewalker, I'd wonder how Big Boss would turn out too. Maybe a part of the "decent into villainy thing" was him condoning to create a doppleganger of himself while he's free to create Zanzibar Land with no obstruction. In that way he betrayed Kaz too. But I agree with you about the story's theme consistency. It seems off.
Too bad this is probably the last one. There's really a lot left out of this story. Played MG2 recently and something doesn't seem to add up - like Big Boss being a cyborg. Kojima might've retconned this one.