It's your opinion and it's not bound to what I believe, but as it's open to opinions, I would write mine as well. I agree on Danzo, he has good writing behind him but your opinions about blurring the line is largely made up and without any merit at all. From the start, Danzo was shown in a negative light; a man who clawed his way up and used whatever method necessary to have his way. The fact that he had trophies embedded into his arm and that he was directly involved in the assassination of a NGO Organization leader than was a proponent of International peace is something beyond the basic term Evil - these actions personify it.
Danzo, for the better word, represents the Evil of Ninja System. You have to be ridiculously blind-sided by fanboyism to not see the logic in this. In fact, one of your favourite characters (Kabuto) was a direct victim of Danzo's schemes - the same cunning scheme that ended the life of an innocent woman who was sheltering so many children with no homes and families. These are some of the many surface realities within the realm of manga that completely over-turn your fusion logic - they obliterate it.
I would disagree with Itachi being a symbol of layered characterization is well. Frankly speaking, I have never understood this at all. The guy is defined through his Jingoistic ideals that are not even his own but they festered in his mind through the 'Will of Fire' sham that runs deep within every individual's mind. All of the citizens are forever tethered to this and Itachi represents the pinnacle of national fanaticism. A character so clung to Nationalism screams poor writing.
Anyhow, I agree with the rest. Here are some of my choices -
- Sasuke and Nagato - Sasuke represents Freedom and Self in this entire scheme of things. Whatever he did, he chose to do so in regards to the presented circumstances. He possesses human frailties and perseveres to reach all his goals, deliberating, weighing, and contemplating along the way.
He is a universalized image of what children go through in war torn areas. The hate and helplessness that plagues them. Sasuke along with Nagato are the only two characters that carry a sense of verisimilitude into the manga in regards to wars and their ugly and cruel repercussions. Their characters challenge the preconceived notions surrounding patriotism and nationalism by bringing in the ideals of Self-Preservation and Freedom from the warped ideals that surround a Nation and the segregation faced by select individuals. To exclude these characters from well-written list is quite distasteful. Quite.
Neji and Lee - Neji was such a character that presented another facet of freedom in regards to Clan segregation, something that was fully realized with Sasuke. He brought out the ethos that any man can create his own destiny, away from the roles that define him. It was a beautiful metaphor that was never culminated by the author. It always disgusts me.
Lee was another such character whose persona was every man's story. He was ordinary and yet he desired extraordinary. That is every man's tale, which is way I am always fond of Lee.
Other Honorable Mentions -
- Sasori - This character is just bloody brilliant. I cannot stress this enough. His entire existence is a perfect paradox - a mortal in an immortal body, which itself is completely dead. The doll would never age, which is why Sasori stresses upon the beauty of puppets. The doll is ageless as it's dead, but the soul that resides him is metaphorically aging but immortal as well. Brilliant, just brilliant.
These are all I can think of, I'm afraid. Might add more.