There would be two sorts of ethical considerations there when a new opportunity such as efficient eugenics presents itself. One could be dubbed ethical inertia: since X was impossible before for mere mortals, making it possible now is playing God, and thus bad. This is the sort of thing that wears off if X turns out to be beneficial... Many a thing related to agriculture and preventative and life-saving medicine, for example, has moved from playing God to doing what is necessary, desirable and even one's moral obligation.
It's the other half of the ethical equation that truly warrants discussion. That is, the judging of X by its perceived consequences, both direct and indirect. And even though we have practiced eugenics on "lower life forms" for thousands of years, we have very little idea what the effects would be on a lifeform that doesn't have a supervising God like ourselves. We can watch thoroughbred dog breeds wither and die and make adjustments to the breeding program as the result. But who's gonna watch us when we screw up big time in a breeding experiment of global scale?
Eugenics would probably be relevant to the species only if practiced on such a scale. But in practice, one would do eugenics on a small subset of the population, leaving a "survival pool" to take over if the experiment fails spectacularly. I see little ethical problem with that as such - but there is a major problem if the two groups are treated dissimilarly in terms other than interbreeding rights. Eugenics is unlikely to produce a Master Race biologically, but the very act of practicing eugenics is likely to produce such a thing socially. And that, I think, is The Thing about eugenics, ethically speaking. Not breeding laws, not abortions or other fetus screening or manipulation techniques, but the general social consequences.
GATTACA portrayed a relatively benign society in that the thoroughbred class supposedly got dibs on jobs and perks solely on the basis of the results of their breeding. It was a classic meritocracy, and it only happened to miss on what merits it valued - the protagonist's initiative and drive was obviously a trait that should have been favored and made a eugenics priority!
However, it would be more likely and far more frightening that a society would favor thoroughbreds on the basis of the history of their breeding. You don't have to be a superior specimen in order to get the job, you only need to be a eugenically selected one. And you don't have to be an inferior specimen to lose out in the race, you only need to lack a history of eugenics. A real society wouldn't have machines that tell your excellence from your blood sample, it would have "citizen files" that would be unable to record the abilities of the individual, and development thereof, accurately and in real time.
The more general ethics of meritocracy vs. ideals of equality are not related/limited to eugenics as such, IMHO.
Timo Saloniemi