Humans lose brain cells all the time and aren't adversely affected unless they lose A LOT, so I wonder how many "braintrees" could be deforested without harming the "Aiwah" sentience(s?)................ a few hundred? a few thousand? 1%? 10%? 50%?
it wasnt the braintrees only, it was everything on the planet... well... all the planets... so... depending on the effeciency of the 'system' and how much capacity it is using, im guessing 10% would cause an impact... maybe not a massive one, but one nonetheless... unless the remaining trees can somehow compensate for the loss...
Are the braintrees even a sentience, or do they just store data?
if we've learnt anything from movies like Terminator, when you store enough data in an advanced system, eventually it becomes sentient of its own accord. Give something thoughts and it can think. that said, i think your later question about how Aiwah controls animals suggests in itself some sort of sentience.
And is the Doc's actual consciousness bouncing around somewhere in there, or just her memories? Did the transfer even take?
we dont know if the transfer took, though i think it is implied later when the main character (mental block with his name) tells Aiwah to look inside the docs memories and understand how dangerous the humans are... also... when the doc was dying at the end, she said something like "i can see Aiwah (excuse the paraphrasing)" so its an assumption her consciousness was trasnferred and reformatted to become part of Aiwah...
And what about Na'avi that have been dead for a while before getting uploaded? Can the braintrees pull memories or even consciousness from half-decomposed grey matter?
i doubt it... it would be like putting a bullet through a hard drive and trying to read data off it later...
How do the braintrees exert their influence over the moon's animal life? Do the birds and bears "link" with the "I/O willow" trees like the Na'avi do? Or are they attuned to the trees' electrical communications somehow?
good question, some of the animals didnt even have the neural connection the na'vi and certain other animals had, as far as we could see... perhaps there was some kind of physical manipulation, like changing magnetic fields to make those hammerhead rhino things stampede in a particular direction, or the animals that did have a neural link sheparded the ones that didnt... however, soem form of 'wireless' connection is the most understandable and lore-friendly explanation, even if there was no evidence of it...
This "linking" ability....... how limited/powerful is it? Can Na'avi link with other Na'avi? Is it possible to transfer memory, thoughts, or even entire consciounsesses through the link? (I know that it works that way with the braintrees, but what about other species?) And can whatever abilities there are work if one or both "ends" are dead, unwilling, or unconscious? Jake seems to mentally overpower one of the "Banshees", and the big red one later...............
when jake and the na'vi girl do the horizontal monster mash, their pony tails link, so evidently possible... though somesort of tradition would indicate its not to be done unless 2 people are rather intimate... as for overpowering, that was the whole idea, that you use your will to command the animal... but it also has a bit of religious inference there, Aiwah put the na'vi there to be the caretakers and benefactors of the forest, like god did to adam and eve etc. so the logical inference is that the na'vi are 'intelligent' (having made tools) and therefore can overpower the instincts of other animals. at the very least though, you could assume its some sort of symbiotic union where you and the animal share thoughts and so understand each other better and work better as a team...
How many humans were allowed to stay behind? We only see three (counting Jake) but that seems rather low for a colony that apparently has thousands of workers, it's own factories and labs, and such a large defense contingent...........
couldnt tell you, although i think it was only those 3 or so who aided the uprising... they werent allowed to stay on to run the factory etc, they were allowed to stay because they were friends of the na'vi
What are the remaining humans who either don't have avatars or don't want to swap to them full-time going to do? They could only really live on the base without quickly running out of whatever the masks use as an airscrubber or becoming something's lunch, but I doubt that the Na'avi would be too keen to keep the place up and running.....
from memory it took 5 years to grow an avatar... and not everyone was compatible with it, even if your DNA was used to make it... i think that is one of the lose ends you generally get when a movie wraps up... everyone is so happy that the bad guy was defeated that no one thinks about what happens next... anyway, alot of the structures used by the humans seemed to have a rather long life span, as did those air scrubbers... so i assume they would come to some sort of arrangement whereby the facilities could be cycled to aid the humans... idn... like i said, loose end...
Just how smart are these braintrees? They don't seem to know or care when the humans start bulldozing, and they could have done their whole biosphere-in-revolt thing when the "invasion" first landed. (This suggests that they can lose a lot of their individual parts before becoming affected: would you let the miniature aliens walk around with relative impunity if they were slowly lobotomizing you?)
it may not be a matter of smart so much as inclination... if you are a complete pacifist, you must let someone kill you without putting up a fight because that requires violence and then you rent a pacifist anymore... Aiwah is sentience, though i doubt she thinks like humans or even Na'vi do...
ANYWAY, i really liked the movie, like space age, more sophisticated version of Pocahontas... i also bought the videogame... in and of itself the game isnt great, but its got some nice features and gameplay and the graphics arent bad... its more for the extra story than the game itself, but, if you liked the movie, you might as well get the game just so you can fly a banshee or a scorpion tilt-rotor or even the dragon gunship 
