I have long beleived that one problem for the U.S. EPA's position in Massachusetts v. EPA was that it was difficult to square the federal government's litigating position with various statements, reports, and actions taken by the federal government related to climate change. Particualrly insofar as the case boiled down to whether the EPA could reasonably conclude that greenhouse gases pose a sufficent risk to justify regulation under the Act.
Under Section 202(a)(1), the EPA is required tp regulate automotive emissions of air pollutants that "in his [the EPA Adminsitrator's] judgment cause, or contribute to, air pollution which may reasonably be anticiapted to endanger public health or welfare." Whatever one thinks of climate change, it is indisputable that the EPA, and other federal agencies, have issued statements about the risks of climate chagne for years. This was not lost on the majority in Massachusetts v. EPA. As Justice Stevens wrote for the Court:
We moreover attach considerable significance to EPA's"agree[ment] with the President that 'we must address the issue of global climate change,'" 68 Fed. Reg. 52929 (quoting remarks announcing Clear Skies and Global Climate Initiatives, 2002 Public Papers of George W. Bush, Vol. 1, Feb. 14, p. 227 (2004)), and to EPA's ardent support for various voluntary emission-reduction programs, 68 Fed. Reg. 52932. As Judge Tatel observed in dissent below, "EPA would presumably not bother with such efforts if itthought emissions reductions would have no discernable impact on future global warming." 415 F. 3d, at 66.This quote (on page 23) comes from Justice Stevens discussion of standing, but it is signficiatn nonetheless. At the end of the day, I believe it was difficult for the Court to credit some of the EPA's arguments given other things the EPA and other federal agencies were saying, and had been saying for years.