1. A foreigner who joins the natives and becomes their saviour
2. A pristine planet inhabited by primitive natives
3. A cloned alien body which can synch with the human pilot's mind via computers
Now I will address these points and give you my view on why they are very disturbing
1. The white saviour is perhaps the most unforgivable flaw to be found in this movie. It is the unadulterated Western fantasy, redeeming the White man for the sins of colonialism by becoming one with the natives, and then proceeding to outdo them at all of their own traditions, becoming a messiah figure, saving them from the evil of his own people. This is deeply insulting, suggesting that the natives are incapable of understanding the issues in greater perspective, an ability reserved only for the interloper. Especially if we compare the main character in Avatar to the young warrior leader of the Na'vi, we see that the Na'vi leader is blindly belligerent, without any introspection or thought. Meanwhile, the human hero is able to understand the right course of action due to his more rational approach. Its classic orientalism through and through, the irrational, bellicose native and the rational Western man, who is prepared to fight, but reluctantly. In addition, we get a nice dose of sexual imperialism thrown in, with the messiah figure easily seducing the chief's beautiful daughter. It is essentially a retelling of the Pocahontas narrative without any nuance.
Another feature that I would like to highlight is the natives pony tail thing. This allows them to 'sync' with the animals and plants of Pandora. It seems like a wonderful idea, everything able to communicate completely and thus live in harmony right? When looked at from another perspective, it illustrates the true loss of our connection with nature. Part of the miracle of man's ability to connect with nature, for example a horse and rider, or even just any of us communing with the trees for a moment, is the totally intuitive nature of that relationship. There is no tangible connection. The horse and rider always remain somewhat of a mystery to one another, which makes those moments of intuitive understanding so magical. The trees never objectively talk to us. We hear them intuitively, subjectively. On Pandora, these mysteries have been reduced to simple, technocentric gadgets, everyone having a universal format "USB" dangling from their head, allowing them to truly connect. This is part of the theme found in this movie which basically tells us our reality is insufficient.
2. One thing comes to mind here, one is the propagation of the noble savage myth. Sure, indigenous peoples deserve our respect and historically, they did suffer in the worst way. That being said, it is highly problematic to portray them as these sublime, infallible people who are deeply connected with every aspect of nature. It is no doubt a flattering portrayal of the natives but at the same time does an injustice to the historical reality and to the multidimensionality of a culture. Obviously the aliens are fictional and thus we can just write everything off to creative license, but the fact that this archetype is such a cliche motif means that we have to recognize that this is a trope and it is being resurrected here.
In addition, as Jared Diamond points out in "Collapse", indigenous cultures are no less fallible than any human society. Many indigenous cultures wreaked havoc on their environments, destroying them and rendering once fertile lands barren. It is not a disgrace to any culture, merely an outcome which is quite common anywhere humans live.
Finally, I believe that the beautiful world found in Avatar, while clearly meant to inspire us to protect our own planet, is actually the death knell of widespread environmentalism. This is due to the fact that the underlying message is that our world is not interesting enough to save. It used to be that we could depict the beauties of our own natural world as a rallying cry to save the planet. The fact that this is now insufficient illustrates the fact that people have truly given up on our own world.