Naruto is better than 95% of the shounen jump stories but it havea lot of things it done wrong and it could be so much better.
I sure agree with that, it's far from perfect.
But it's also the only goddamn manga that made me cry. You imagine how much empathy you feel towards being of papers to actually cry when they die?
Naruto had many flaws, but it was great in terms of characters-building. The "bad guys" all had their own motives, their own past, and everything made sense in that area.
It stopped making sense when Nagato revived everyone. I can understand Naruto forgiving him, but not Nagato being talked out of it on such a scale.
After that, there were more and more mistakes. That's true.
So, of course, now that Kishi has the experience of a long-running manga, he can prepare better, especially if he doesn't draw (which is a shame, I like his style a lot...). We'll get new characters with a super interesting backstory and new motives. And a whole new setting.
And as they say, you learn from your mistakes. I'm sure Kishi knew that Naruto had flaws.