Well, there can be multiple reasons about why eugenics won't work.
The first problem is related to pleiotropy of human genes. That is, one gene can control multiple traits, although the influence of a single such gene on a particular feature may be small. So eugenic practices will very likely pick out some characters caused by pleiotropic genes and amplify desired alleles in the gene pool, but there may be other anomalous traits linked with the very same gene. Thus eugenics introduces new problems in this scenario.
(Some afterthoughts: These antagonistically pleiotropic genes are not uncommon, and they could be rationalized from an evolutionary perspective. Some traits encoded by such genes may be beneficial to the organism in its early life but not later. Such benefits, if they come before sexual reproduction, confer greater fitness to that organism. An classic example is the sickle cell anemia. Heterozygotes have resistance to malaria while homozygotes suffered from reduced life expectancy.)
Then, it's easily understood that eugenic programs shall proceed slowly in comparison to Morgan's fruit fly experiment, for example, as a result of the extended period between birth and sexual maturity for our species. Therefore, we have to wait for decades to have some real accumulation of beneficial phenotypes.
Finally, critics of eugenics widely believe that it will sacrifice genetic variety. This argument makes sense because those desired phenotypes are chosen by us, not by nature, so they are not necessarily those best assist our survival. Though we live in comfortable environment nowadays, there may be plagues, droughts, and other large-scale natural disasters in far future that select against our chosen traits. If our species is too homogenized then by eugenics, we will probably face a grave situation...
1.Carter, Ashley JR; Nguyen, Andrew Q. (2011-01-01). "Antagonistic pleiotropy as a widespread mechanism for the maintenance of polymorphic disease alleles". BMC Medical Genetics. 12: 160. doi:10.1186/1471-2350-12-160. ISSN 1471-2350. PMC 3254080 Freely accessible. PMID 22151998
2.Richard Lynn, The Science of Human Diversity: A History of the Pioneer Fund (University Press of America, 2001 ISBN 978-0761820406).
(Since this topic is really controversial, extreme care is needed to choose evidences to support the answer. For those who may disagree, please put a comment below about your opinion instead of immediately casting a down vote, thanks!)