To answer some of your questions:
For the last question, read Lord of the Flies the situations are very similar and I would guess kids have only ways to act without adult supervision and not being fully mature to realize what needs to be done rather than fullfilment of desires (even though if it is wanting to protect someone, it's still wanting)
why Blue's way worked, I guess he was the intermediate (notice the order of people in charge in the series, Zwei (too liberal, rules aren't enforced), Blue (somewhere in between and most mature of the leaders, knew when to push his way around and when to turn blind eye, also had separate agenda from the others) and Ikumi (too strict, didn't leave any liberties to general populace, too oppressive) at least that's my take on it.
as far as the fundamentals or morals (unless i'm misunderstanding), I thing that's left to viewer's interpretation. "know when to stop, but fight when must fight" "Stick to the golden middle"
Love this one "You tried your best and you failed. The lesson is - never try".
Anyway it's been over a year since i've seen the series and that's all I can remember for now.