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In the beginning of FLCL, Naota is a young 13 year old boy who seeks to be an adult. The color palette of his outfit is a light teal, indicating a carefree mentality, despite being self-serious.
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By the end of the show, Naota has relaxed a lot and this shows in his muted clothes here. He is no longer excessively trying to so maturity, and instead has a chill demeanor.
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Haruko is a wacky and fun-loving spirit who never misses a chance to bust Naota's chops. Her bright outfit and appearance reflect this.
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When it is revealed that she's using Naota for her own gain, the muted colors mirror her vicious personality, especially considering the animation here.
