This is an argument I've been toying with for a while, and I haven't yet seen it in print, but I imagine it's not entirely novel.
What is the strongest argument in favor of being pro-choice on abortion? In my mind, it's something like this: There is significant moral disagreement about the permissibility of abortion. Thus, it is inappropriate for the state to intervene and attempt to make the decision in place of the individual woman. Those who think abortion is unjustifiable can elect not to have abortions, while those who think it's permissible can choose otherwise if they so desire.
In other words, on issues for which there is significant moral disagreement (especially when the decisions predominantly affect only a single family), individuals should be given the right to decide for themselves whether to perform the action in question. (I'm setting aside here all of the other arguments for and against the permissibility of abortion, as well as many of the details about particular cases.)
Consider genetic engineering now. There is significant moral disagreement on this issue (the population is not as evenly split, but around a quarter of people in the US claim to have no problem with it generally, and even greater percentages are in favor of it in limited circumstances). It does not matter what the arguments provided on one side or the other happen to be. If reproductive freedom is something we wish to guarantee in the United States, then we must leave it up to individual parents to decide how to augment their future children.
In short, the cases are almost exactly analogous. Both are decisions that almost entirely affect only the parents and the potential child. In both cases, there is a hostile opposition to reproductive freedom that seeks to make controversial moral decisions for people, denying individuals the right to choose. If there's a difference, abortion is probably more morally suspect, because no one denies that (all other things being equal) it is better not to kill an animal or person, while genetic enhancement will, if safe and effective, only improve a person.
My suspicion is that the real opposition to biotechnological enhancement comes from emotions like disgust and fear. (Leon Kass, my arch-nemesis, actually admits this, with all his nonsense about the "wisdom" of the "yuck factor". Oh, so cleaning toilets is morally wrong, Mr. Kass?) I'll put it simply: if you're against enhancement of any particular sort, then don't do it. But you don't get to decide for me if I feel otherwise.
To summarize: abortion and genetic engineering (not to mention other technologies like in vitro fertilization, pre-implantation genetic diagnosis, and genetic screening) are morally analogous cases. For someone who is pro-choice on abortion to be anti-choice on genetic engineering, they must demonstrate that there is a morally relevant difference between the two cases. Otherwise they are just hypocrites, like all those pro-lifers they are so averse to.
One possible difference is that, while abortion (at most) can remove genes from the gene pool, it cannot add new ones, like genetic engineering could. But, this is not a morally relevant difference. Mutations occur naturally all the time, and they can lead to novel genes as much as our intentional interventions could. Does that make mutation wrong?
Let me anticipate one final objection: "There is a morally relevant difference," claims my hypothetical adversary, "insofar as genetic engineering does not only affect one family. Genetic engineering could lead to lasting changes in the genetic make-up of humanity, while abortion could not."
There are many problems with such objections, but the biggest is a general ignorance of biology. I think it's a misunderstanding of at least three central concepts: evolution, species, and the relation between genotype and phenotype.
Wikipedia has a decent one sentence summary of the first: "evolution is change in the genetic material of a population of organisms from one generation to the next". Evolution has no direction, although we might (with a tremendous effort) be able to give it one. Evolution occurs whether a genetic change is "natural" or artificial. The only difference is that we have control over the artificial changes, but the "natural" ones are largely matters of chance (guided by selective forces, of course). Humanity is constantly evolving, whether we like it or not.
Second, species are not stable entities. Again, Wikipedia says this about species (while admitting that it is not universally agreed upon by biologists): "A common definition is that of a group of organisms capable of interbreeding and producing fertile offspring of both genders, and separated from other such groups with which interbreeding does not (normally) happen." There is no stable core to a species by which it can be identified, because evolution is constantly altering the composition of a species' gene pool. Further, because there is so much variation within species, it would be hard to identify "human nature" or any animal nature even for a single point in time. To "change human nature" would require a large-scale, significant change. This is not something in the foreseeable future.
Lastly, far too many people are genetic determinists, even if they hate biology. In short, genes are only half the story. Throughout human history, we have been altering the phenotypes that appear in persons through environmental interventions like education. No one objects to these. But if we talk about altering genotype, which will have no guaranteed affect on phenotype, just as a person who attends school is by no means guaranteed to actually learn something.
So, to respond to our objector: It is unlikely that a species-level change could occur with these technologies, but even if such a thing is possible, it's not necessarily a bad thing. Species are constantly evolving, and so we're going to change one way or the other. Why not try to direct this change positively instead of leaving things up to Lady Luck and her cruel genetic lottery?