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well... i would choose Angela/Ashe from Kuroshitsuji. since it is an angle you would think that it would be the hero but in reality it dose more damage trying to purify souls then to let the world be
then number two would be Azula (i know avatar is a cartoon but its art is based on anime so) since she tries to control people through fear due to her mommy problems in the past she seem like the villain that you almost want to sympathies for