If you liked
Shinseiki Evangelion Movie: Air/Magokoro wo, Kimi ni
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...then you might like
Koukyoushihen Eureka Seven: Pocket ga Niji de Ippai
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Both movies are derived from series full of religious and mystical symbolism. Both are about a conflicted adolescent boy piloting an alien bio-mech, in love with a half-alien/half-human girl, who come to conclusions about authority, their own identity, and their love in the middle of a prophesied apocalypse.