It's simple, first-year law school stuff. Regulation follows the statute and where there is a conflict the administrative agency must bend to the will of Congress. So the EPA must ultimately comply, as best it can, with the scriptures contained in the federal law. The problem here is that the Clean Air Act is two generations old-- it was first passed in 1963 and has been amended only twice, the last time in 1990-- and there have been great strides since then in the science of pollution (and the eagerness of the American population to regulate it).
By trying to fit new ideas into old law, therefore, the EPA will open itself up to legitimate legal challenges about the scope of its power to regulate greenhouse gases under a law that was not explicitly designed to allow it to do so. And those legal challenges would come after the lengthy regulatory process (notice, comment, etc.) that marks the creation of any new significant administrative measures. In other words, if the Obama Administration chooses to restrict emissions through EPA regulation it may take years for those restrictions to go into effect.
If, on the other hand, the White House goes to Congress and seeks to amend the Clean Air Act to expressly cover carbon dioxide and other greenhouse pollutants the process may move more quickly. Strong amendments to the Act would embolden the EPA, allow it to move quickly to enforce the new restrictions, and generally preclude federal judges from gutting the measures at some point down the road. The risk in going the legislative route, of course, is that there appear to be enough opponents of the new restrictions—both Republican and Democrat—to muddy the amendments or even to delay a vote.
There is also the chicken and egg problem. If the Obama Administration goes first to Congress to seek amendments, and fails to get them, the EPA will have a tougher time arguing in court that it already has the power to regulate greenhouse gases under existing law. "If you already have the power," a federal judge surely would say at that point, "then why did you go to Congress in the first place?" It's because of situations like this that I am thankful I don't get a vote in Congress, at the White House, or in the corridors of administrative agencies.