Jake arrives and gets put in the science team. The original point of having him be the Colonel's man on the inside can stay - what conflict this plot has is going to be between the humans, since the Planetmind is too big to engage in any visually effective way, and the intrahuman conflict seems perfect for this setup. The marines are not bad people in any sense - certainly not the genocidal maniacs of the original movie - they're just soldiers dealing with a situation they don't understand and which makes their ostensible job very, very hard. They're there to be bodyguards for people who they aren't very similar to to begin with* and who will slowly but inevitably go off the deep end down on the planet. The marines go out in HEV kit and hardsuits; most of them have probably never touched a native Pandoran lifeform with their bare skin, let alone started channeling the Planetmind. The Colonel, in this story, doesn't have to be the bloodthirsty maniac of the original movie, he's just legitimately worried about what is happening down on the planet. The people behind the expedition back home think getting the transferal technology working reliably is worth a little temporary crazy on Pandora, and if all else fails it has been demonstrated the weird can't get off-planet; the Colonel probably agrees with the former but since it's his brains the zombie hordes will be eating if things go south, he's understandably less reassured by the latter. He doesn't start blowing things up in the climax because he's being paid to, or because he likes to do it; he's blowing things up because his first and most vital priority is to defend humanity, and when things speed up in the third act he's honestly afraid that this thing is now able to jump planet, get back to Earth and destroy civilization as we know it. In this context, Jake is not an intel source in the Na'vi - who cares about the Na'vi? they have stone knives and bearskins - but is the Colonel's own personal attempt to feel out what is going on the planet and just how dangerous it is. He's long since stopped trusting the scientists** but a marine, more psychologically distant from the planet to begin with and loyal to the Colonel, not the project, is a perfect tool for this job.
Finally, the real plot of the movie gets started. On his first trip out he gets separated as originally, runs into Neytiri, who thinks "huh, he's a hunter. Sexy", which feedbacks into Jake, who looks at this three-meter critter with secondary eyes and four shoulderblades and also thinks "sexy" as well. When he gets back, this freaks him out a lot, freaks out the scientists not at all (the Na'vi don't think science is sexy in particular, but they've all had similar inexplicable emotional reactions) and the Colonel is worried that Jake is going downhill so fast but also interested in the fact that it happened so fast around the Na'vi specifically. Jake gets sent back out.
Jake comes back with Neytiri to the village and starts acclimatizing as in the original movie. This part can run essentially the same, although we need to get rid of the mobile Avatar lab - that's certainly not happing in this set up - and add some more of Jake having trouble dealing with everyone back at base. The videologs should not just get increasingly sympathetic to the Na'vi - they should get increasingly disjointed and irrational as well. The Colonel, with the "help" of Jake and some figuring about data transmission rates, adds the big trees to his contingency plan of Things To Blow Up When it All Goes To Hell.
Jake gets inducted into the tribe. This involves linking him into the tribe and (since it hasn't been done to an Avatar before) Grace comes along to watch, as do a couple of marines. Jake links in and Gets It: he figures out the whole planetmind thing and, before he goes completely around the bend, manages to convey enough of this to Grace that she gets it, too. Unfortunately for them, the marines and Na'vi are already keying each other up to a ridiculous degree and violence breaks out. Jake and Grace join in because, after all this time in the field and this close to the big tree, neither of them can think of any good reasons not to. The marines are killed. The Colonel hard-unplugs Grace (who's trying to explain things but the Colonel, for obvious reasons, isn't listening) and Jake, who's human body is now braindead. Between the fact that Jake is gone, he's murdered two marines, and Grace's ravings about the planetmind, the Colonel decides it's time to go to Plan Z.
The Hometree gets blown up as in the movie, which causes pretty much all of the scientists to freak, so the Colonel (ostensibly and possibly even actually for their safety) ships them up the Elevator. Grace, the other recent-arrival avatar-driver, and the pilot escape, Grace gets shot, and they all take off to meet up with the Na'vi, who of course (along with everything else) are riding the ragged edge of going absolutely berserk. They try to transfer Grace, fail, and then decide to go on the warpath. (This means we can drop the "Jake rides the giant bird" subplot, and good riddance, too - Mighty Whitey is a pretty sketchy trope to be playing straight these days.) The Na'vi attack, synched up with the giant horde of animals, hits the compound. We have the main climactic battle again, although kind of different - the Pandorans have the giant animal horde but the humans are defending a fortified point, not attacking without electronics. Call it a pyrrhic victory for the natives. At the climax, Sully and the Colonel fight, Sully wins (of course) and then cuts the Cable. There's nobody left down at the bottom, and the cable is slightly unstable now that it's not quite as long as it used to be (the center of gravity is barely above geosynch now, but it is a little), so Sully (although given his state, more probably other-Avatar-driver guy) negotiates with the guys at the top****.
Since the humans have finally figured out what's going on, they (or at least the scientists) have had an aha moment where everything makes sense, and since the military types are in a pretty terrible strategic situation, they negotiate. (It's probably not necessary to actually show the negotiations - just have the Cable get cut, Jake gets on radio, "I think we need to talk", jumpcut.) Then we go to the denouement/epilogue, with Jake's v.o. explaining how things have been patched up with the humans, who still have a small presence here but a lot more careful about not ticking off the Planetmind. Jake runs around happily with the Na'vi, roll credits.
So that's my version of Avatar. As you can see, it drifts a lot in theme and message from the original, and really by the end probably owes as much to Stanislaw Lem's Solaris as to the actual movie Avatar. But I certainly think it would make a good sf movie.
*The marines are jocks, the scientists are nerds. That's not enough to cause movie-worthy conflict between grown adults, but it's enough to start off some baseline tension; these people are from different tribes. Example: the marines probably r&r with typical space-marine movie r&r, drinking and arm-wrestling and whatnot; the scientists mess around with the computers and play games (which has the added bonus that when you start losing badly at chess because you can no longer strategize well, its time to start watching you; when you stop connecting with the concept of "board game", it's time for a brachial full of tranqs and a fast ride into orbit). Another example, even if it would take some good writing to convey it in the movie: the marines are based out of orbit and think of themselves as being on tour on the ground even if they spend weeks at a time down there; the scientists are based out of Base Camp and think of themselves as taking trips into orbit even when their time is distributed the other way around. The scientists driving the Avatars - even before the psychological changes set in - start to think of themselves as living in the woods and occasionally stuffing food into the body back in the prefabs.
** The main problem with this setup is it leaves no room for Grace***. She's not that important plot-wise but is very important in providing exposition for the planet and a voice for the project, and somebody with that much Avatar time in the new setting would have long since been shipped back home. My best guess is that she should be the head of the main science team - the ones who don't use Avatars, since they need some science types to stay stable, run the machines and psych tests and so on. If they treat Avataring like radiation poisoning, she might also just be severely rationing her time out in the field, showing each team of new arrivals around but only briefly.
***As the Calvinist said to the Roman Catholic.
**** Negotiating an ending is important, since otherwise another starship shows up in 12 years and drops depleted uranium rods the size of telephone poles on every large tree on the planet.
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