One of the biggest offenders for this was the whole "achieving world peace" Kishimoto gave Jiraiya and later Naruto during their confrontation with Nagato. A lofty goal that is incredibly complex to accomplish. It seemed like Kishimoto was developing Naruto by challenging his mindset and patience through Nagato destroying Konoha and killing many of his friends. With Naruto showing mercy to him and showing the audience that he could be the one to lead the ninja world to true peace (especially when compared to Sasuke who decides to murder shit)
...but in their meeting when Nagato ask him how will Naruto achieve peace, Naruto says I dunno but I'll keep trying while showing him the book of the person Nagato ruthlessly murdered with no problem.
...and Nagato is ok with this answer
...so he gives his life to revive everyone he killed in the village
...and Konan gives him some paper flowers and walks away
...and the whole "world peace" quest is barely mentioned again by Naruto
At the end of series it's like you said, barely anything changed. The ninja system is the same old thing, except now we got modern/futuristic tech so mission accomplished?
Basically Kishimoto loves to implement complex themes but always gives them simplistic solutions
Yeah, Nagato throwing away his entire ideology he's been following for 20 something years and just accepted Naruto's non-answer irked me even back then.