Smudboy claimed that 'it's all a dream' points to bad writing. I disagree. It's bad writing when it's no more than a reset button, but it does fit with the Protheans trying to teach paragon boy scout (tm) a lesson in not being able to win.
The whole psychological play makes much more sense with the supposed original ending of it being a 'dream' invoked by the Eden Prime beacon.
You would simply have Shep wake up and see boy scout being gone from his / her eyes, making the change the Protheans were convinced of being 'correct' a fact. Why else would there be a Prothean who by ME1 rules should not have been able to survive at all?
They shouldn't have changed the ending just because it leaked early.