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If you bad guys had been destroyed and the goodies all survived, yes, it would have been one hell of a lame ending. However, having all the good guys destroyed is just the same thing inversed. It's a common assumption that something is original if it has a dark ending, simply because the vast majority of stories end on a positive note.
The fact that Mario finally destroyed Boo by destroying himself was the creative part of the idea, but I think it should have had more emphasis.
That aside, the use of music in places was excellent and the direction was great too. I would critisize the narrative though, for a 10 miute long movie very little seemed to be happening. There was a fight and then the deaths, that was about it.
Still, definately an interesting movie.