I really understand where you're coming from. Normally, stories work in such a way that we grow to despise the villains as much as protagonists do, for example, when Freezer killed Krillin in DB. That was like, you know, all of us turning Super Saiyan along with Goku. But in Naruto, just when we come to hate the villain (and I'm speaking for those of us who don't worry about: "Oh, is it a human? or a drawn character that doesn't exist?"), turns out we end up with the villain's flashback and an explanation of why did he end up being the way he was. So now we kind of feel for him too, and he's not that much of a villain anymore... It's like, the thing with loving and hating someone is that, when you stop doing it, it feels like the fun's over. I remember people being hyped about Lee during his fight with Gaara and even after that... But then the Kishimoto Dragon Ball style came to the picture and many characters, including potential villains, were lost because of it.
However, I still think that depth is definitely more valuable than classic good versus evil. If I had stayed a child, perhaps Naruto would be so boring for me in terms of principles. Because I didn't even worry about that. Bad guy is bad, good guy is good, and the good guy is the one I have to look up to. But what can I say? The more I grew up, the more mistakes in life I made, and the more I wanted to feel like I could be forgiven, and like I could also be loved even though I was wrong many times. This is what I love from Naruto. Even with its funny plot holes and its contradictions, I still love it and I will still keep following it until the end, no matter what.