First, the ruling repeatedly cites minority positions, especially those dissents expressly written by Stephen Breyer, as if they were binding caselaw. That is a remarkable appeal to the vanity of the liberals on the higher court, where they surely see this going ("Steve: we're going to pretend that your dissent is as important as the actual law.")
The other is that in order to circumvent a well established Constitutional precedent -- that states have no standing to sue the Federal government on behalf of their citizens -- they have invented a novel circumvention in which the states are given standing by virtue of suing on behalf of state institutions.
Specifically, the Court accepts the notion that WA and MN have standing because of a claim that the inability of academics to travel to various hell-holes such as Yemen damages their prestige. This is breathtaking: not only have the states shown no actual harm -- only an anticipated one -- there is no precedent that I'm aware of that a plaintiff without standing can sue on behalf of someone else who also doesn't have it. (The state institutions don't have it, because their anticipation of harm is not evidence of actual harm.)
We might also ask, since the Court seems impressed by the failure of the Trump administration to show that terrorists have actually come to the US from these countries, why they are not equally impressed by the failure of the plaintiffs to prove that ANY faculty member has ever even travelled to Syria. This is all the more puzzling because the principle of primacy of the political branches in making and applying immigration law actually forces the court to presume WITHOUT evidence that the former is true, while the consideration of the lack of evidence for the latter is a presumptive test for the supposed likelihood that the plaintiff will prevail.
In other words, they have have shifted the burden of proof to the political branches, and made them answerable for political decisions to the courts. That is, in a word: bullshit.
This decision is on a level of Dred-Scott-awful.
One of the main conspirators in the first WTC plot was Iraqi, and Najibullah Zazi is from Afghanistan.