I think the Mechanicus would have a fun time looking at the 'hive mind'-esque communication of the biosphere. I can see many, many tonnes of de-foliant, and Hellhounds/Banewolves aplenty if the Imperium were to claim the world.
Apart from the technology of the Imperium being better than that in the film (although I haven't actually seen it, so I'm going off what I've seen in clips and heard about in reviews), the big difference would be the attitude. There would be no buggering about with trying to infiltrate the Na'avi and messing with them from inside- rather the Imperium's army would be told to smash in, take the ground and not to worry about who, or what, got hurt and or killed in the process. Casualties, on the Human side, would be immaterial; casualties on the Na'vi side would probably be more important as the Magi Biologis would really want to see what the deal was.
There would be no need for extremes such as Exterminatus (of any flavour) as the threat posed by the inhabitants of Pandora (that's an arse name, on a par with unobtanium!) would be absolutely zero to a committed Imperial colonisation attempt.
GFP