Notice, if you understood everything in Naruto and everything was that simple, what would be the benefit of people creating threads to try and explain things or you figuring something out.
What would be the fun in predicting something to happen or something which hasnt happend or cant happen.
One reason some people enjoy Naruto is because of its mystery, you dont really know what Kishi is thinking and its going.
Every week people try to predict what is going to happen to the story, and it doesnt turn out that way.
These people tend to feel browken hearted or surprised. Those that take it well, praise the manga, those who dont take it so well, say the manga is a flop.U_U
Also, people have their expectations, when the story doesnt go in line with their expectation, they tend to flame the storyline.
I say to such one,try and write a manga and see how many people would give attention to it.xd
IMO, just enjoy the story as it goes, Kishi has his own storyline and would explain things as time goes on.
Some of the points you stated have already been xplained, some are yet to be explained but in all Naruto is a great manga and need to be appreciated.