Update on my previous post:
The nationwide injunction issue isn't actually raised in this case because it was brought under the APA. The statutory remedy when an agency exceeds its authority is that the court vacates the agency's rule. (There's also the somewhat controversial practice of "remand without vacatur," but that's pretty rare.) That means that the effect is necessarily nationwide.
This is different from what a court does when it "strikes down" a law passed by Congress. In the popular imagination, courts tell Congress to basically delete an unconstitutional law from the U.S. Code, but what's actually happening is that the court is simply adjudicating a dispute. If the court determines that a law that, on its face, seems to apply to the dispute is actually unconstitutional, then the court adjudicates the dispute without relying on the unconstitutional law. But courts don't have any supervisory authority to tell Congress to get rid of its bad laws. And Congress is almost never a party to lawsuits involving the constitutionality of statutes anyway, unless it's participating as an amicus. By contrast, when challenging an allegedly illegal agency regulation, the agency is usually the adverse party, and if you win, the law actually commands the court to "set aside" the agency's unlawful rule.
The court's opinion is worth a read. Regardless of whether you agree with it (personally, I think it's a close call), it's carefully reasoned and covers a lot of interesting issues. This is not some shoot-from-the-hip senior judge who's just gonna do whatever he wants to do.