Such considerations, however, aren’t sufficient of themselves to justify the administration’s decision to stop defending DOMA against constitutional challenges in federal court. A weighty separation of powers issue comes into play. Under normal circumstances, the executive branch has a constitutional duty to enforce legislation passed by congress and signed into law by the president. That duty has traditionally been interpreted as encompassing the defense of any statute in court as to which there's a reasonable argument in favor of its constitutionality. The administration can hardly argue that DOMA doesn’t meet that standard since it has been upholding its constitutionality in federal courts for the last two years.
Seen in this light, Obama's decision not to make reasonable legal arguments in court in behalf of a duly enacted statute amounts to an ominous power grab by the executive branch from a legislative branch that isn't inclined to repeal DOMA. Here's Orin Kerr, laying out the issue better than I can (my emphasis):
Granted, administrations have always enjoyed ample discretion when it comes to deciding when and where to fight their legal battles. But that discretion has never been so likely to be abused in the service of partisan objectives. This administration’s evasiveness about the constitutionality of DADT before it was repealed and Republican state attorneys general sudden receptiveness to a novel interpretation of the commerce clause that would eviscerate ObamaCare suggest that partisan politicians have never had a harder time distinguishing between the wisdom and the constitutionality of laws they oppose. Whatever you think about DOMA's constitutionality, the administration's decision not to uphold it is another symptom of the law's becoming a political weapon.[“T]he Obama Administration has moved the goalposts of the usual role of the Executive branch in defending statutes. Instead of requiring DOJ to defend the constitutionality of all federal statutes if it has a reasonable basis to do so, the new approach invests within DOJ a power to conduct an independent constitutional review of the issues, to decide the main issues in the case — in this case, the degree of scrutiny for gay rights issues — and then, upon deciding the main issue, to decide if there is a reasonable basis for arguing the other side. If you take that view, the Executive Branch essentially has the power to decide what legislation it will defend based on whatever views of the Constitution are popular or associated with that Administration. It changes the role of the Executive branch in defending litigation from the traditional dutiful servant of Congress to major institutional player with a great deal of discretion.
“If that approach becomes widely adopted, then it would seem to bring a considerable power shift to the Executive Branch. . . . If Congress passes legislation on a largely party-line vote, the losing side just has to fashion some constitutional theories for why the legislation is unconstitutional and then wait for its side to win the Presidency. As soon as its side wins the Presidency, activists on its side can file constitutional challenges based on the theories; the Executive branch can adopt the theories and conclude that, based on the theories, the legislation is unconstitutional; and then the challenges to the legislation will go undefended.”