Even though Avatar is not the most unique story ever told, I think there are some really surprising elements to it.
Though I think that both Jake and Neytiri are generic characters (not annoyingly so but not worthy to be included in my Hot People in Science Fiction lists), I think that there were still some spectacular moments of gender bending that make Avatar a little more interesting than just a panorama of beautiful imagery (which I believe is an integral part of story telling; actually, I think the story which the images tell is what saves this film from being merely shrugworthy). I thought it was really interesting when the father told Neytiri to protect The People, since in earthling perspectives, the role of protector is usually masculine, something that is passed down from father to son. I also think it's interesting in the scope of Na'vi culture as well - after all, if I understand it correctly, Neytiri was supposed to inherit her mother's role as the spiritual leader, not the role of her father.
Another moment that I appreciate for its gender bending is here:
So often (not so much now, I suppose, especially in science fiction, but I think it's still a popular perception) you see images of women as weak - frail, swooning into the arms of a masculine presence (James Cooper, I'm glaring at you). The conception is that men protect women, the fairer vessel. But here, the roles are reversed. It's Jake who is weak, Neytiri who is supporting him, protecting him.
I find it to be a beautiful image, possibly my favorite element of the movie. Not only because of it's gender bending -- it's just...tender, accepting -- I see you -- I grok you, acknowledging an individual, a person, something that exemplifies the very best of us.