I would just like to point out that though it is commonly and erroneously proported to be "The Five Stages of Dying", Dr. Kübler-Ross' model was actually supposed to be a model for the emotional stages of those close to the terminal party accepting that person's death. Not someone accepting their own. So I highly doubt it is Link working through his own death, as is commonly proposed by advocates of any of the types of "it's all in his mind" theories.
I could see it as being a metaphorical way to tell the story of how he got over and accepted Navi's departure. That doesn't mean though that MM was a dream or whatever. But yeah I agree.