I'd say that Avatar is simply a classic story, and that race is the least of its themes.
Principly it has a strong environmental message, a few sly jabs about the Iraq War and as usual in Cameron's movies a few jabs at mega-corps and their lack of morals in conducting their business.
This is all that really needs to be said. However simplistic or not you feel the movie tells its messages, it is largely about two things, neither of them race:
The first is its specific environmental message. More than just "don't do bad things to nature" its specific message is that industrialized civilization dismisses nature as an obstacle in the way of its own perception of expansion, progress, and especially in a capitalistic society, profits. In a particular moment in the film, a scientist tries to explain what is happening with Pandora's unusual biosphere and that it's not "pagan nonsense" but real science. The corporate exec listening interrupts and blurts out "what are you people smoking? They're just trees!"
There is a statement here on human beings being willfully blind to facts that are inconvenient to themselves and while this kind of thinking impacts every facet of life, humanity's interaction with the natural world has been especially impacted. There's no way you'll ever be able to talk about such ideas without causing some people a kneejerk reaction against "noble savage" tropes or "the simple pure life" stereotypes. But just because something is a trope or a stereotype doesn't necessarily mean there isn't a kernel of truth in it.
A lot of people with loathe this movie because it goes big to make its point and that will seem too simplistic. However, to give James Cameron some credit, there are some key moments he gets right in making his point. The afformentioned dialog points out the difference between reacting with stereotypical dismissal towards vague new age nature worship" - a popular thing for people to do, and an attractive straw man argument -and confusing it respect for the environment backed up by rationalism and science. For all the movie may be cartoonish - not necessarily a bad thing in transmitting a message, however much many folks hate that - its hung on a few solid principles.
Secondly, the corporate, government, and money messages are themes Cameron has been on about for years. In Terminator, Skynet came about because of military-industrial complex collusion. Skynet then attacked humanity because it instantly concluded that the human organizations that created it could not be trusted. Ironically, Skynet had a point even if nuking the Earth flat was a bit of an overreaction. In The Abyss, military men are sent to investigate potential alien contact armed with nukes and orders to take them out just to be sure. In Titanic, the rich and wealthy, the backbone investors of governments who help keep regimes in power, are shown to be trite and decadent, concerned with triviality, image, and prestige over basic human needs.
On another note, it's pretty clear that another of the filmmakers' aims with Avatar was to help the message by making people fall in love with the alien world. For all it is harsh and dangerous - which in a way, defuses protests that the story romanticizes nature in a simplistic way - it is also beautiful and strings are tugged to make the viewer feel terrible when parts of it are bulldozed for no reason other than carelessness. The intentional simplicity of the story aids this goal. Making the Na'vi "flawed" in the same way that real life peoples that have been oppressed were flawed, would have been "complex and realistic" but also would have shifted the viewer's attention onto the sociopolitical drama and away from just plain feeling awful when the corporate bastards started kicking alien puppies.
Also, I do have to wonder - do people who think the movie is unrealistically simplistic also think that, given the opportunity, the scenario the movie outlines would never happen? I mean, really. The flip side of the simplification coin is that while, say, the native american peoples may have done bad things on their own terms, that doesn't make it any less bad what colonials did to them. I find it interesting when some people seem to try and distract attention from core messages by focusing on complications that may not be relevant to the point at hand.
Some have even called Avatar more of a kid's movie. That's interesting too. If it is partially a kid's movie - sure is violent for a kid's movie, but I digress - then its very simplicity and broad strokes will do a good job of imparting its message on kids. I'm not entirely clear on how the basic message of "don't be a dick and burn down people's crap because you can make money off it" is bad.
In the end it could just be that such topics are inherently too contentious in the present social climate where it seems everyone is on a razor's edge about issues such as environmentalism, corporatism, and the like. And those issues have been heavily politicized. I wonder how films that are cited as being superior with the same themes Avatar uses would be received if released today - and what viewers would read in that wasn't there.
Hell, District 9, which now that we have this movie to compare it to, was initially slammed by lots of kneejerks because of all sorts of simplistic and "racist" overtones in in. Funny enough, now I'm seeing tons of people holding up District 9 as the "right way" to do it compared to Avatar.
"LOL."