At first, it may seem like the reason why Jake Sully was screwing around on ( and even deciding to stay on) Pandora instead of doing his mission was because of Neytiri, but in reality, it's because it's the only time he ever gets to being on his own legs instead of being in a wheelchair.
The trees "talking" to Jake doesn't make a lot of sense, unless you look at the funeral scene (the one that was on for about ten seconds). Earlier it is established that the trees connect to each other with tree "nerves", and can connect with someone's mind. In the funeral scene, Neytiri plants a seed of the sacred tree in the grave. The trees then must hook into a person's brain, and read their memories, and play them back for anyone willing to listen.
Naming the planet 'Pandora' seems kind of random, until you find out that the oldest and heaviest known organism on earth is a giant quaking aspen root system. The thing covers 106 acres, an entire forest of aspen trees that are really all one single plant. This plant's name? Pando, which means "I spread." Pandora isn't named after a mythological woman who opened a box. It is named after Pando, the Earth version of Pandora's forest.
Jake's personality underwent a major shift over the course of the movie, particularly because of his experience time as his Avatar. But then you remember, it's not his Avatar, but his brother's, who could easily have been a much different kind of person, which transferred to his Na'vi body when they duplicated his neural relay.
If the unobtanium is a Room-Temperature Superconductor, then an obvious use is as low-resistance high-voltage cable. This would dramatically decrease power demands. It could reduce pollution, or if not, it would free up power reserves to be used by people who hadn't previously had access, raising living standards. This could explain why humanity wanted unobtanium so badly.
At first it's rather strange to see how trained horseback archers and hunters like the Na'vi would blindly charge at a firing line of sec-op forces, rather than flank them, until one remembers that this is how they actualy start their hunts on larger beasts. They get them into motion via a stampede and then pick out single targets by driving them away from the main group. Which is most likely how they expected their tactics to work against the human soldiers.
The entire film is much smarter than it appears and a handful of plot points give hints of a much more interesting story that only one human character even begins to understand:
James Cameron is a hard sci-fi nerd who put a lot of thought in to the physics of the star ship and the other minutiae of the film, but he's also a knowledgeable biologist (who spent the proceeds of the movie on a deep sea scientific expedition). He would not have overlooked simple issues like the appearance and function of the Na'vi.
The Na'vi appear extremely humanoid compared to the other life on the planet and whilst they are not the only 4-limbed beings, it is an extremely unusual body plan on the planet. The odds of the Na'vi and humans looking so similar are astronomically low.
Grace mentions that the trees are connected in a network orders of magnitude larger and more complex than a human brain and these trees are capable of interfacing with the Na'vi, she is hinting that the biosphere of Pandora is a single giant hyper-intelligent consciousness (Eywa).
The Na'vi appear to have admin privileges over other life on the planet, using a universal connector that lets them control other life forms but not visa versa. They can also connect to the tree of souls to commune with the `Spirit` of the planet.
Together this paints a very different picture of the story, making it much more than Dances with Wolves in space. Pandora (or at least a large portion of its arboreal biosphere, maybe just one continent?) is alive, hyper-intelligent and capable of manipulating the rest of the ecosystem to fulfil certain functions. Humans arrived decades ago presumably in a much smaller ship before the events of the film, the round trip taking several years, the lethality of the planet probably killed some of them before they encountered their first Na'vi, because at the time, the Na'vi didn't exist. The planet studied the human remains and created mouthpieces that it could use to communicate with the humans which it called the Na'vi, it created a custom-made ambassador species. It explains a lot of strange things such as why humans were able to create the Avatars program in the first place (because Eywa had already met them half way before they even began).
This changes the meaning of everything in the film including the films title; Avatar is a reference to the Na'vi, not the human project. The `upload` of Grace and Sully gives Eywa full access to the memories of a very intelligent human and a more average one.
On a darker note, it explains why the humans were allowed to leave at the end (the planetary equivalent of giving native Americans blankets infected with smallpox) as Eywa can't travel in space, the only weapons it has that can strike at Earth is a custom-made biological weapon which it can smuggle back with the human survivors. Because as it knows from absorbing Jake and Grace's minds that humans have the potential to at least cause wide-spread destruction from high orbit if it realised that the trees themselves were a threat.
At the end of the movie, Jake's consciousness is permanently transferred into his Avatar. Okay, how did Eywa do that? Align all the Avatar's neurons in a way so they contained Jake's personality and memories etc.? Whatever happened to Jake's original body then? If Jake's consciousness was copied and pasted into the Avatar, there's nothing to suggest the human couldn't have continued to live on after this was done, as a human Jake next to the Na'vi Jake. To complete the job, you essentially have to euthanize the original human body. And it leaves you wondering if the Jake in the avatar is still the same person, what with all his central neurons having been replaced. A case of the 'Theseus Ship' Problem.
It's heavily implied the world-brain is magic, or at least so far beyond human understanding as makes no difference.
The process of extracting someone's complete personality may render their original brain non-viable, leaving their former body dead or an empty husk. Or Eywa may switch off its respiratory process once the extraction is finished, to spare the Na'vi from having to do it and to accede to the subject's wish not to continue life as that body anymore.
It seems to be implied that the Avatar process doesn't duplicate a consciousness, it transfers it. When the human mind moves into the Avatar, the original body falls unconscious. What Eywa did is essentially a permanent form of that, so it would have left his human body in a coma anyway.
Knowing the official background material like the Avatar Survival Guide or the official wikia, reveals a large list of problems that any human who remained on Pandora and can't permanently switch into an Avatar body will have, because of the massive logistic required for humans to survive. Meaning those who sided with the Na'vi like Norm, Max and the rest of the research team might be very well doomed together with a lot of other personnel of the base. Major problems are:
Each supply ship can carry only 200 people home, while the base is implied to have a staff numbering in the thousand. Meaning there are hundreds of people trapped on Pandora. There are also 6 new ships scheduled to arrive on Pandora over the next 6 years, carrying another 200 people. These ships can not be stopped and require resources from the planet to start their way back home. These ships are also the source of most complex material used in the base, from machine parts created on board to material transported from Earth that can't be created locally. Without the mining the RDA might simply cancel any future flights dooming the entire base.
Having a kilometer long ship with an anti-matter reaction drive and a fusion reactor stranded in Orbit alone is a huge nightmare inducing though.
The base requires a large number of logistics personnel to stay operational. Fixing and maintaining machinery and computers, cleaning air filters, operating the reactor, operating the communication systems, repairing and maintaining structures and many more jobs must be filled. This raises the question how many of these people were on the side of the science personnel who helped the Na'vi and are now trapped on the planet?
There are also a large number of miners, which might not be all too happy about having lost their jobs and being trapped on the planet.
The armed security personnel was actually necessary to protect the entire base from wildlife. Including all kinds flying monstrosities who would eat humans for breakfast. Really they're the only thing standing between the non-military personal and the rest of the entire ecosphere. They also secured flight sectors for the Valkyrie shuttles to land, which adds to the problem of bringing the next 1200 people coming over the next 6 years planetside.
The planet's extremely resilent plant life was prevented from overgrowing the entire base and destroying its structures by burning everything down around the base wall with acid on a regular basis. Said acid being a byproduct of the mining. Without the mining, there is no acid. Without acid, the plant life will destroy the only shelter the humans have.
First, The Avatar bodies are completely unnecessary and a waste of money/ resources for their plan to get Unobtanium for Pandora. This is because the Na'vi can recognise that the human-controlled avatar bodies are fake Na'vi; the humans have learned the Na'vi dialect and taught them how to speak human languages (at least, English); and even if Pandora's atmosphere is unbreathable for humans, they have masks that provide breathable air, along with hovercoptors and shuttles to deal with the hostile native predators. They could take a hovercoptor to the Na'vi settlements and simply talk to them.
The contact group which piloted the avatars hadn't ever claimed they were real Na'vi in the first place, they just wanted to understand and be understood by them well enough to help smooth relations. It was a high-tech version of diplomats dressing in the clothing of the country they're negotiating with, the better to put their counterparts at their ease and demonstrate (truthfully or not) empathy and respect for the host culture.
Second, Jake never tells the Na'vi why the humans are on Pandora. All he had to say was what the humans wanted (magnetic rocks) and why (according to Word of God, humanity in this movie have ruined Earth's environment and need the Unobtanium to power starships to find other habitable planets). Then they could've worked out a solution.
This second point is debatable. It's made clear that (the Na'vi's primary home) is planted directly on the biggest deposit of the desired mineral. To ask the Na'vi to make way would be like a mining company coming in and asking for you to move out of your well-established home so they can mine. Humans may be flexible enough to move in such circumstances, but the tree has more significance to the Na'vi than simply being a home. It's highly doubtful they would've moved, even if they could've explained this to them.
That said, it's entirely plausible that with all the advanced technology going around, the Na'vi could have led them to a less gigantic but still entirely useful source of unobtanium. They could even do what colonists did in Africa and the New World and try to get the local tribe to fight against the others, and then take the unobtanium from the soul trees of their new enemies. The tribal differences between the Na'vi shown in the movie are big enough that someone, somewhere, probably has enemies they wouldn't mind selling out to the invaders with big guns. Not such a nice story, but it's more practical.
Three words that render the movie's entire premise redundant: sub-surface mining.
Could be hard to plan for if the rocks you're digging for are only being held down by the rock layers you're digging through. How much use is existing know-how about mining techniques supposed to be at averting mine collapses, if half the material that's collapsing is falling up?
Every creature on Pandora seems to possess six limbs (or wings) and their nostrils located on their chest. The Na'vi on the other hand, possess only 4 limbs and their nostrils located on their face? Why exactly are they so physiologically different from the other lifeforms on Pandora?
You forgot the prolemuris, and, in addition, NOT all creatures are 6-limbed, the ikran being the prime example other than the aforementioned.
The creatures that showed four limbs, one set dividing at the elbow, is apparently a good picture of the evolutionary ancestor; some kept splitting for more limbs, some merged, and that one stayed the same. Or at least, there's the Word of God.
Possibly the evolutionary lineage that led from the prolemuris to the Na'vi went through a semi-aquatic phase in the past, which made positioning of the nostrils higher on the body more advantageous for catching a breath at the surface without exposing one's whole upper torso. Same reason why crocodiles have their nostrils aiming upwards rather than forewards, and cetaceans' are on top of their heads.
Grace, for Buddha's sake. Powers of ten are not good arguments. They're not even good ways to express numbers. When Selfridge wants some reason not to bulldoze the tree of souls, why not explain that it contains unique biomaterial that's so far beyond any human technology it might as well be magic? Magic that if examined carefully could be reproduced and maybe become the biggest discovery since the wheel, which the company would own. Shove a 500-page research paper under his nose just to show him exactly how much there is he doesn't understand about what he's doing, needs to read up on before he can make an informed decision. You want to delay the slaughter at least a day or two, it wouldn't be hard if you used actual arguments.
Considering he's simply in it for profit and he clearly doesn't care one whit for the science involved, she really should have just told him that the tree is "like an organic computer" and the only one of it's kind they've found, making it priceless. She could claim that with study, it could be replicated and patented (which considering it's similarities to the Avatar technology, seems likely), which would have far more easily convinced him to not chop it down.
Sadly we missed out on hearing Sigourney Weaver argue that "they could be worth millions to the bio-weapons division" in this film...
That the soul trees are on the biggest and richest unobtainium deposits isn't simply unfortunate: it's inevitable. Unobtainium is a room-temperature superconductor, and unobtainium components in the trees are the only explanation for their biocomputer-like properties. And for a soul tree to grow, it would need unobtainium-rich soil.
It's probably necessary that the mega-trees grow in such soils, and incorporate trace unobtainium into their supportive tissues, just to grow as gigantic as they do without crushing their own trunks. Most of their bulk is held up by magnetism, same as the floating islands.
We're repeatedly told Earth's environment is totally ruined, Jake flat-out says the humans killed their equivalent of Eywa. Yet Jake is an experienced jungle fighter, as are many of the security guys.
There is also the fact that there are BOOKS being sold, including Grace's own doorstopper of a Guide, in addition to other paper products being shown or implied. Grace also smokes old fashioned looking cigarettes, which are given to her in a branded box. Meaning a tobacco industry still exists.
Earth doesn't have an equivalent to Eywa. He's being poetic and exaggerating. He's not saying the absolute truth of the matter.
Similarly, it's hard to call Jake and any of the marines "jungle fighters", considering his initial bewilderment at the jungle environment on Pandora (in addition to the alien plants) and his first outing has him running for his life in a matter of seconds! He only becomes a decent fighter once he trains with the Na'vi and becomes familiar with the terrain and environment. Likewise, if the RDA were experienced in fighting in rainforests, they sure would have won a long time ago?
They could all be experts in jungle warfare on Earth and it wouldn't have made a damn bit a of difference for two reasons. One, there did not seem to be much war going on until the events of the film itself. Two, its Pandora, also known as a portal to hell. There are "cats" that close to being as tall as a human being, if not larger, standing normally. Similar predators on Earth are much smaller. This place appears to be actively trying to kill you. The fact that the RDA expedition has survived at all should be considered a great achievement.
What this troper would like to know is, if Avatar bodies are constructed from human and Na'vi genetic material, where did RDA acquire the Na'vi material in the first place?
The film clarifies that humans have been on Pandora for years before Jake gets there. The Avatars are a science project combined with attempts at diplomacy, that were obviously created long after humans first arrived.
Grace calling Jake "numb nuts." The scene reads like she's making a playful dig, but that's actually a really cruel thing to call a paraplegic. (This was actually mentioned on the Rifftrax of the movie, but it's still a valid point)