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Naruto is probably losing popularity because Kishimoto spent a whole year in Part 2 without showing anything particularly impressive out of him at all. So far his growth over the past 3 years seems pretty pathetic. By using Kyuubi powerups as a plot mechanic to make him seem comparable to the main villains, Kishimoto is making him look like a chump in his normal form.
In a nutshell, Sasuke is still popular because he hasn't disappointed anyone.
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