There are essentially four reasons that the ACA cases are probably the biggest to come before the Supreme Court in a generation: (1) the political consequences; (2) the implications for the Court as an institution and its role in our constitutional system; (3) the consequences for public policy; and (4) the consequences for constitutional law. These cases rate highly along all four dimensions.
The question of the constitutionality of the minimum coverage provision probably rates higher than the Medicaid question on (1) and (2). The individual mandate has come to symbolize the ACA, and even the administration concedes it is "central" to the Act--an Act that is the central legislative achievement of the incumbent President, who is in the heat of a reelection campaign. The political ramifications--though perhaps unclear--will be substantial. Further, whether the Court (for the first time in nearly 80 years) is willing to invalidate a hugely important federal regulatory program as exceeding Congress's enumerated powers will speak volumes about the Court's conception of its role. To be sure, as a doctrinal matter, it is well established that the Court can decide the breadth of Congress's commerce and taxing powers. But the ACA is not the Gun-Free School Zones Act. Nor is it § 13981 of the Violence Against Women Act. At stake is legislation infinitely more important. So the willingness of the justices to exert their authority to check Congress here will say a great deal about the Court as an institution.
On points (3) and (4), though, I think the Medicaid question is more significant, perhaps by a wide margin. As to policy, Medicaid stands as perhaps the most significant social welfare program in the Nation (along with Medicare and Social Security). No doubt, it is the most significant redistributive program, as it only aids the poor and the disabled. Roughly half of the coverage expansion contemplated by the ACA will be achieved through its expansion of Medicaid, extending insurance to roughly 18 million more Americans per year. If this goes away, it will be a very big deal. Moreover, it is not easy to see how a decision that invalidates the Act's Medicaid expansion would not, in some way, endanger Medicaid as it existed prior to the ACA. (The sums provided by the federal government to the States are nearly the same, and thus arguably just as coercive.) Needless to say, a decision that jeopardized Medicaid more generally would be a huge policy development.
And such a decision would mark the first time in its history that the Court invalidated a cooperative spending program on the ground that it "coerced" the States. Depending on what exactly the opinion says, it could well impose significant constraints on many programs--both those that already exist (such as the massive educational funding the federal government provides the States) and those potentially to be enacted in the future.
A decision invalidating the individual mandate will probably be quite narrow and cabined, pinned to its rather distinctive characteristics. Given the political costs, it is hard to imagine Congress imposing purchasing mandates on a regular basis. Thus, the impact on constitutional law, in this sense, would likely be small. But the implications of invalidating the ACA's Medicaid expansion would be hard to constrain, no matter how hard the Court might try. Thus, I think its impact on constitutional law would actually be more significant in the long run.
In the end, then, though most of the smoke has surrounded the minimum coverage provision, the Medicaid issue might provide the real fire.