Manga is lacking the importance of 'ninja'.
I re-watched the original series and saw how the plot goes in-depth on how the structure of a Shinobi society is built on, and how it reflects one's level of expertise.
Genin < Chunin < Jonin < Hokage;
Well, now that's cute. Naruto is stronger than Minato now. So he is past Hokage level. But he's a genin. Weakest level of ninja.
If you want to stay logical, Ino is stronger than Naruto. Cause she's chunin right?
The fact that all matters is that the tailed beast corrupts the ninja system. Jinkuuri's shouldn't be involved in ninja academy, rather build and learn from Jonin. That way, in time of war, they are born ready to take cautionary action.
I'm definitely sure that most characters are OP. Kishimoto is un-impressed on how he makes his characters. He lets off one flaw, he has to make another character who can counter him.
tl;dr: The Ninja system doesnt really matter in shippuden.