This is a landmark case and will have impact across the entire legal spectrum for many years.
As a non lawyer, I think the plaintiffs failed to effectively argue (ignored) the tax issue. Many decisions have been based on the intent of Congress. In this case the Congressional Record clearly indicates that Congress intended the "tax" to be a penalty. Had the Plaintiffs spent more time rebutting the Tax argument , Justice Roberts would have had the means to invalidate item IV.