In the introduction scene, a child Navi is shot. And your enemies, the RDA, use guns. You have a choice whether you use guns or traditional weapons (bows, spears, etc)
In certain locations where Thanators spawn, they will stalk you and eventually attack if you don't leave briskly. You cannot use your sense ability, and there is a white fog at the edges of the screen when this happens.
Eywa is a big part of the Avatar series as a whole. She is discussed a lot ingame, and if you recklessly hurt nature too much, other Navi will not like you for a while for not following her
The Sarentu children (protagonist and some allies) were taken from their clan at a young age and forced to learn and adopt human things, to manipulate them against their own people. If they acted out, they are punished or killed
The RDA takes and does unethical experiments on the Pandora wildlife, causing them to become irreversibly erratic and traumatized. They cannot be saved, you have to kill them