They claim they had nothing to do with the story aspect and wanted to change things about it. However, Team Ninja probably had more to do with the mediocre gameplay too.
well we all know they had something to do with that!
this is kind of an interesting take on it
http://sparkylurkdragon.tumblr.com/post/19133543752/dissecting-other-m-a-dream-interpretation
just like FFVIII, bad writing will always lead to "it was all a dream" theories. regardless of it being BS, if I were sakamoto I would take this and run with it