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AlfredoTurkey said:
Because developers want to force us to press the buttons they want us to press. I can't tell you how frustrating it was playing the early MGS games and having to use the O button instead of the X button.

That is the standard button layout in Japan. Developers were just to lazy to change it for western release. Also Nintendo does this for their consoles in the west as well. A button (confirmation) on Nintendo controllers is B button (cancel) on Xbox controllers.