I think that every character has a moral in it.
Naruto's story is basically "be true to yourself" and "work hard".
Pain's is "don't get corrupted by the world" (this one applies more so to idealists, like he was)
Minato's is "Sometimes you have to sacrifice yourself for the greater good"
Itachi's is "Don't try to do everything yourself" and "Lying to your little brother about why you killed your entire clan is a very bad idea"
Itachi also has a great quote that I think sums up the story as a whole.
"People live their lives bound by what they accept as correct and true. That's how they define "reality". But what does it mean to be "correct" or "true"? Merely vague concepts… their "reality" may all be a mirage. Can we consider them to simply be living in their own world, shaped by their beliefs?"
In the end, its a story about people and our flaws, and how that makes us beautiful.
XD I'm a sentimental one.