Majora was the evil spirit contained within the mask. the thing that was using the Skull Kid as a puppet. the thing that then took over the moon and said "I shall consume. Consume...everything." the thing later incarnated by the three forms of the final boss.

as I see it, Ganondorf was just a guy that was corrupted by power, and was constantly seeking more of it to the point that it disfigured him and the world around him. Majora was inherently evil, and wanted destruction.