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This is very much a split-the-baby decision. The Obama administration can claim that the act was upheld, and it was although it was narrowed in one specific case.

The opponents can claim a clear victory because a majority held that the individual mandate was outside Congress's commerce power. The act was upheld on a narrow majority on the basis of the taxing power instead. This means they can never impose criminal or even civil sanctions for not buying health insurance (and it isn't clear to me if the floor to the penalty is Constitutional under this reading).

The states also came out as clear winners. The court held, 7-2, that states cannot be compelled to join the new program by threatening them with loss of their entire Medicaid funds. In other words, if a state wants to opt out of the expansion because they don't want to pay administration costs, of if they no longer want to participate in SCHIP, DHHS can only deny them the funds for that program, not all of Medicaid. Every major expansion that is reasonably separable now is a separate program. This is a big defeat for the federal government here and a big win for the states.

The line-up on the Medicaid issue surprised me. If it were to be 7-2, I would have expected Breyer and Ginsberg to be the dissenters, but instead it was Ginsberg and Sotomayor. That Breyer sided for states rights here is one of the greatest surprises I have seen in recent years.

tl; dr: The act is upheld, but the court has struck a couple of significant blows to federal power and we haven't by any means heard the end of this.