Most of you need to realize that Kaguya has ninjutsu cancellation abilities. Naruto has Senjutsu, Sasuke doesn't. Put Naruto in Sasuke's shoes and all of his attacks would be cancelled as well. Naruto is not more powerful than Sasuke. I would like anyone to prove me wrong. If Sasuke is not getting through Kaguya, that doesn't mean Naruto is past his ability.
Sasuke on the other hand has the additional power of intuition. That makes his character far well-rounded and versatile. I am not surprised that Kaguya was scared, as her first step was to separate Sasuke from Naruto.