I know this thread is a bit deja vu, but I thought I'd weight in to add that I've been running it much like otakusensei seems to be, working from the assumption of a racially/demographically mixed, but culturally assimilated/integrated and supportive NAN population. A great many citizens have few or very iffy blood ties to the relevant Native cultures, but nonetheless self-identify as part of the modern incarnations of those cultures. I realize that conflicts with some of the early canon, but I have some of the same logical issues with that canon that others in this thread who don't like the NAN are bringing up.
I do think it's a damn cool idea, but it's one that needs some thematic clarity in its execution. Regardless of the likelihood of any of it happening, if you assume it's just blood natives kicking everybody else out or ruling a conquered population, then that's as much a crime as anything's been, and I want the NAN to be an empowerment thing, and a point of hope, if you'll pardon the phrase, in an otherwise grim setting, a reminder that when the common man gets his shit together, the whole world shakes.
And I also want to simultaneously avoid the "Magical Indian" and "Noble Savage" stereotypes, and that's admittedly pretty hard. I've tried to do that by assuming that the bulk of the magicians trained in the early days were trained under Native tutelage and supported the rebellion, regardless of their own ethnicity; the shamanic elements are not restricted to blood natives. What history I've given out to my players (none of whom were previously terribly familiar with the canon version) has emphasized the mass Awakened elements of the revolution; for instance, a technomancer they crossed into Rapid City in Sioux country to extract was a black woman with Creek tribal affiliation named Michelle Stands-in-Clouds, and digging through her files during the legwork phase, I mentioned that the name originated with her Atlanta grandmother standing up to the tear gas in protests before the heavy fighting started.
I also tried to show the Sioux Nation on that run as still a modern place, even if it has sort of a New Old West feel. The NAN cultures aren't exactly the same as their pre-Indian Wars counterparts because a culture is a living thing, and you can't keep one pressed under glass and expect it to be healthy. They're not running around hunting buffaloes on horseback. There are for sure buffalos, but they're on ranches. The Cherokee that settled in the Rapid City area still are heavily involved in agriculture, but in 2070 it's vertical agriculture in a set of Shiawase-funded crop arcologies and the like. You get the idea.
I also don't want it to be Avatar, where it's still Whitey that has to save the day for the indigenous people, cause that's still a sort of superiority bullshit. I think this is maybe the hardest pitfall to avoid. I've tried my best to make clear that the Native Americans were still the core of the SAIM rebel movement, even if they didn't supply the mass of the boots on the ground. It's the names like Howling Coyote that get bandied around as founding fathers. I think this is maybe the hardest pitfall to avoid, because it's fairly subtle. But I'm trying.
My point is, I don't feel like we should abandon the idea simply because it wasn't executed well early on. It's got promise, I think. Whose game is this, anyways? I don't have to be married to fluff from when I was a preschooler. I'm honestly only really impressed with the fluff I've seen from Catalyst. In before edition wars... The point is, I think the idea of the NAN in the abstract is unique, interesting and valuable well beyond its use in isolating Seattle (we don't even run in Seattle, we run in Minneapolis).
As far as actual Native characters, we have one amongst the PCs I GM for, a full-blood Ojibwe dwarf mercenary named Jukebox from "up north", modern NW Ontario. I kind of tend to imagine her as an Ojibwe version of Revy from Black Lagoon, if that tells you anything about the character. She's easily the most Pink Mohawk character in the current campaign, and has kind of a "no one owns me" natural outlaw vibe. The player's a significant part Ojibwe herself, from northern Minnesota, so it's not entirely an alien culture for her, but she said she wanted to play something other than a "cookie-cutter Ojibwe", and I think she's definitely done that. Much of the drama comes from the fact that she has a sister in Minneapolis' Knight Errant, and Jukebox is definitely the black sheep of the family. Sometimes they help each other, but there's issues from being on the opposite sides of the law.
Interestingly, Jukebox hit it off right away with the NPC Zipper from "On the Run". So far Zipper's backstory I've got elucidated a bit more; grew up in a Cherokee farming arcology to a Japanese father and Cherokee mother in Rapid City. Having a dwarf kid didn't do wonders for the father's career, so he got blackballed, and their relationship was always...awkward. Her being a lesbian didn't make her fit in any better.(Hey, they said it in the module that she was, this isn't some wish fulfillment I'm pulling out of my ass. Hell, Jukebox's player's a straight woman) So a lot of her drama has been related to not getting along with them, as well as the fact that she's kind of spinning her wheels getting her life together. And Jukebox is always getting herself in deep shit, and Zipper worries about her.
Another major NPC from the NAN is a t-bird jammer from the northern border named Turtle¸ a Mohawk Warrior Societies guy. He looks less Indian, but has some in him. He's developed less as a character because the PC who has him as a contact never seems to show up.

Anyways, I feel like the NAN characters that have showed up already have some depth to them beyond just being generic Indians.