I touched on this in another thread, but I think its important enough to warrant it's own discussion.
I find a lot of science fiction using different species of aliens to represent different races/viewpoints/aspects of human kind. This seems to me to be tacitly supporting the notion of
biological determinism, a pseudo-scientific notion that character can be determined entirely by genetics.
Consider the episode of Deep Space Nine where a young Jem'Hadar is raised by humans, yet they ultimately have to let him go because - despite being a fully sentient and rational creature - his 'nature' makes him incapable of living in civilised society. The Star Trek franchise isn't by a long stretch the only culprit of this - it tends to occur in pretty much any character-driven sci-fi featuring aliens.