The Federal Government Is Limited
The US Constitution was designed to limit the power of the Federal government. It is built into the document. The powers of Congress are listed, and changing that list requires a Constitutional amendment. State constitutions tend to give states more power in more areas than Congress has.
People forget that simple fact. Just because a state can do something doesn’t mean that the Federal government can do the same thing. Nixon couldn’t just get Congress to pass a law mandating a 55mph speed limit, he had to threaten the states with a cut-off of Federal highway funds to force the states to do it.
Bmaz at Empty Wheel has a comprehensive post on the issue in Requiem For ACA at SCOTUS & Legitimacy Of Court and Case.
I have never felt that the individual mandate was Constitutional as written. If they had used Medicare buy-in instead of the complicated mess they created, it would have passed muster, because it would have revolved around the Federal government’s taxing authority. The way they did it depends on an expansion in the Commerce clause, and they should have known that it wouldn’t get by the current Supreme Court.