As you can see, there pretty much are some sexist undertones in this story. It’s not malicious on Kishimoto’s part, but the undertones are still there. While there is somewhat of an understanding that there are no specific policies ruling the Narutoverse based on gender — and females are generally treated with respect by their peers and subordinates — they are not always treated as equal to a man by virtue of the dialogue and by their perceptions of women. This is ultimately a reflection on the mangaka.
This is not to say that anyone and everyone complaining wanted the girls/women to overpower ALL the males, let alone surpass Naruto and Sasuke. That is a strawman. It was always understood that Naruto, at the very least, would be among the strongest characters in the end. As Naruto’s rival, the same was true for Sasuke. That was not the issue.