There are a number of issues to consider here.
1. Will the baby be healthy, emotionally and psychologically normal? Will the child be seen as different from his/her peers and therefore ostracized?
2. Will the cost of the procedure lead to a socio-politial situation where the rich engineer "perfect" children and the poor, who do not have this child engineering option, are unable to give their children the same engineering advantage as the rich?
...prenatal genetic modification—the alteration of an embryo’s genes—does not increase reproductive choice for all women, just those who can afford it. (eNotes)
The discrepency between people of varying income levels (the income gap) is already a controversial issue, even in the democratic capitalist nations of the world. What would happen if this gap was given a physical embodiment?
3. Assuming that this procedure would be available to people of all income levels (i.e., free), we should also consider the will of the child.
Children do not have any control over how they are born - with what traits of height, weight, coordination, etc. To some extent these traits will help determine what a person will or will not grow up to be (too short to be a professional athlete; too tall to be a fighter pilot, etc.). Yet we understand that the child will have the ability and the right to choose a personal course of action.
Will this right to choose be mitigated or diminished by the parents' choice of how the child is engineered? If a child's traits are designed before birth, will this limit the child's ability to choose his or her own path in life? What happens when parents choose to serve their own needs instead of the needs of their child? What happens when a new civic eugenics program pops up and a nation-state decides to engineer children for specific tasks, jobs, or social roles?
Is the degree of pre-birth engineering going to equate to post-birth social control?
These are all issues that come up in such a debate. Your concerns and opinions regarding this questions will help you shape your own argument about whether or not parents should be allowed to custom build their babies.
Arguments, both pro and con, are widely published online. For more on the subject of genetic engineering and cloning regarding women's rights, see the articles "Genetic Engineering Threatens Women's Reproductive Choices" and "Genetic Engineering Protect Women's Reproductive Choices" (eNotes).