1. Military protocol: if you're a military pilot or soldier or whatever and you refuse to follow your orders and leave rather than engaging the target, your career is over the minute you get home. Our helicopter pilot girl apparently went undisciplined in any way. I don't buy it, and the plot hinges significantly on her actions.

2. The whole VR/radio thing: Avatar asks us to believe that we can get stupid-low-latency radio communications and staggeringly high bandwidth to a synthetic body that's possibly hundreds or thousands of miles away from the transmitter. We're then asked to believe that there's a particular area where radio communications and whatnot don't work. When our avatars got near this very area, their telepresence seemed to work fine. Again, this was an essential plot element. The whole final climax depends on it, but it doesn't hang together.

2a. Where are the nukes? Assuming the humans really wanted to take out the uber-tree, why dump a palette of conventional explosives out of the back of a cargo transport? Why not use an ICBM of some kind? If radios and whatnot are non-functional, rig up some sort of inertial guidance system. You know, with all that AI that we're supposed to have by then (and which we pretty much already have now).

3. Where's the AI? Given the apparent level of computer technology available to humans at the time, one would think their computers would be much, much better than we've been led to believe. Where are the robots or autonomous aircraft or, for that matter, autonomous mining equipment? How can a pilot just hop into a parked aircraft and take off without some command signal being sent to the thing to ignore the local pilot and head back home?

4. So, like, the whole planet is sentient? Wouldn't that end up looking a whole lot more like the Borg? And what sort of evolutionary process would yield cross-species compatible network jacks?

5. Unobtanium? At least they're honest that it's just a thinly veiled plot device.