1) It features actually alien aliens, with a life cycle more suggestion of actual animals (complete with weaknesses, e.g. sensitivity to cold). This is much much better than the humanoid aliens which low-budget TV shows can at least blame on their budgets, but which bigger-budget films can only blame on lack of imagination, or a desire to insult their audience. Also for some reason those humanoid aliens always seem to want to offer us brotherhood in the great galactic civilization where we can sit around in deep intellectual exchange all day long. Just like Europeans did with Native Americans. And that was within the same species. (For some mealtime deliciousness see below.)
2) The plot is actually well thought-out and contains (largely through Morgan Freeman's grizzled war stories) tantalizing hints of back-stories, placing humans as one species in a whole ecosystem.
3) There is no black and white morality, no heroic portryal of humans, just a struggle for survival. This includes less-than-rational self-interested elements in the human defense force, Morgan Freeman's character prominent among them.
4) There is local New England color invoked in the poetry the alien chooses to recite.
1) The mind-reading/occupying metaphor is taken a little too far. You could cut out all the mental warehouse scenes and the movie wouldn't suffer.
2) From a science fiction concept standpoint, the idea of a universal parasite is a little too easily believed (see Alien or the sure-to-be-awesome upcoming Prometheus). Think about it: yes, we have an alarming amount of effective parasites here on this planet, but even after a billion years of practice to evolve ways to invade and assemble copies of themselves within organisms with whom they share basic building blocks, there still isn't a universal parasite. There still isn't a worm or virus or bacterium equally at home in any vertebrate or even any mammal. Yet here come these guys from across the galaxy, using D-amino acids or a carbohydrate genome for all we know, and they find the human colon completely hospitable the first time they visit one. (I think there's an argument to be made from first principles that if we do encounter parasites that have spread outside their ecosystem of origin, they are likely to be both simpler and more universal than other alien parasites we might encounter. But this is just silly.)