 If you liked
Phantom: Requiem for the Phantom
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 ...then you might like
Suzumiya Haruhi no Shoushitsu
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The settings are considerably different but there are some points in common for both anime:
The high amount of plot twists and the HEAVY similarities between Yuki and Ein, being two apparently emotionless girls being used as tools by a bigger organization, as well as the male protagonist's transformation.