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.
The floating islands may seem like magic at first, but they're actually made out of room temperature super conductor, which is what the humans are there for in the first place. A magnetic material like that actually could levitate (maybe not with all the weight of plants and dirt on top of it, though).
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 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.
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 personal 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 logistic personal 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 personal 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 personal was actually necessary to protect the entire base from wildlife. Including all kinds flying monstrosities who would eat humans for breakfast. Overall being the only thing standing between the none 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.
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.
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.
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?