I almost always prefer subtitled movies, but in anime it's a toss-up. When I watch an animated film, I want to admire the artistry, animation, and background, so I usually watched them dubbed for better story comprehension. In some of the richest animated films, like Akira and Princess Mononoke, there is simply so much delight in watching the screen that being forced to read subtitles would really detract from the experience.
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"And lo, the beast looked upon the face of beauty. And beauty stayed his hand. And from that day on, he was as one dead."