The big one is that this is one of the surprisingly few ninja manga I've read that remembers that ninja are spies and liars. Every single character has ulterior motives (not all of which the reader is privy to), loyalties are often divided, and at least one triple-cross has been sighted. We haven't reached Death Note levels of plots-within-plots (at least not yet), but the constant simmering undercurrent of "I know you're lying to me, but I'll pretend to ignore it because I'm lying to you too" livens up things tremendously. I also enjoy how the "ninja villages" are metaphorical, updated with modern facades (I was amused that one poses as a temp agency). People still use swords and throwing stars a lot, but they also know what guns are.
I also like that these are Ninja Scroll/Basilisk style ninja whose cool esoteric techniques come with awkward drawbacks. As of volume 7 the number of total freaky mutants is pretty low (and even they're more sleek killing machines than misshapen monsters; this does run in the same magazine as Black Butler), but advanced ninjutsu either has morally questionable requirements or messes up the user pretty bad, as in "one of the main characters is quickly going blind and deaf".
Another pleasant surprise is that the women in this series have lots to do. Again, this runs in G-Fantasy, so the hero may well not have any interest in women, which frees them up to actually be supporting cast and participate in the plot instead of just motivating the hero by getting kidnapped or being part of his harem. Quite a few of the villains and walk-on characters from other ninja clans are women too. This pleasantly reminded me of Fullmetal Alchemist (both series also share a habit of randomly breaking the mood with cheap jokes), and I was not too surprised to find out that Kamatani is a woman.
On the other hand, I don't think this series actually passes the Bechdel test, because all the notable female characters I can think of are either trying to help or manipulate the main (male) character (discussing his mysterious powers still counts as talking about him, I think), or are motivated by their devotion to or hate for a man, and there's not really a lot of non-plot-related chit-chat.
I don't want to oversell this series too much; Nabari no Ou is still fundamentally a Teenagers Against Evil manga, with all the tropes and baggage you'd expect if you've ever read one of those, but I'm definitely enjoying it a lot more than I expected to. It takes a couple volumes to warm up, but once it turned that corner I started seeing some promise, and I'm willing to stick around and see how things develop.
