Hmm. There are characters who are (or at least borderline) OP and characters that are not, and there are quite a few variables in the development of a character (both in the naruto universe, and as a story).
genetic (preexisting conditions, such as natural affinities to elements, stamina and chakra production, etc.) and environmental influences (Being taught how to properly use ones abilities, training, etc)
you will also notice that many of the strongest characters are related by blood to the source of all ninjutsu, and that others are powerful from the so6p's actions (bjuu's), hell even both (Naruto ^_^)
There are many paths to gaining power, its a matter of who and how they get there, and franking many people just dont get so far. but for those that do, how its done most def be kept on the down low.
It should be the duty of a village to really monitor the the development of all its ninja, to prevent traitors, as well as the spreading of secrets im sure that they do this to the best of their abilities, but obviously that doesnt always go so well.