The bottom line is that the original intent of the Commernce Clause was not to empower Congress to regulate the growing of wheat, marijuana, or anything else.
For any argument of "Necessary and Proper" to be legitmate it has to be done in pursuit of a legitimate exercise of the power it's being used in support of.
"It is to the following effect. — The constitution is one of limited and enumerated powers; and none of them can be rightfully exercised. beyond the scope of the objects, specified in those powers. It is not disputed, that, when the power is given, all the appropriate means to carry it into effect are included. Neither is it disputed, that the laying of duties is, or may be an appropriate means of regulating commerce. But the question is a very different one, whether, under pretence of an exercise of the power to regulate commerce, congress may in fact impose duties for objects wholly distinct from commerce. The question comes to this, whether a power, exclusively for the regulation of commerce, is a power for the regulation of manufactures? The statement of such a question would seem to involve its own answer. Can a power, granted for one purpose, be transferred to another? If it can, where is the limitation in the constitution? Are not commerce and manufactures as distinct, as commerce and agriculture? If they are, how can a power to regulate one arise from a power to regulate the other? It is true, that commerce and manufactures are, or may be, intimately connected with each other. A regulation of one may injuriously or beneficially affect the other. But that is not the point in controversy. It is, whether congress has a right to regulate that, which is not committed to it, under a power, which is committed to it, simply because there is, or may be an intimate connexion between the powers. If this were admitted, the enumeration of the powers of congress would be wholly unnecessary and nugatory. Agriculture, colonies, capital, machinery, the wages of labour, the profits of stock, the rents of land, the punctual performance of contracts, and the diffusion of knowledge would all be within the scope of the power; for all of them bear an intimate relation to commerce. The result would be, that the powers of congress would embrace the widest extent of legislative functions, to the utter demolition of all constitutional boundaries between the state and national governments."
Joseph Story
Commentaries on the Constitution
The world of difference lies in the fact that Scalia’s argument can be brought into line with Story’s whereas the majority opinion cannot. The huge difference in what Scalia did is that he referenced back to the document itself and sought a way to make sense of the problem in light of the Constitution. I agree completely that his resolution of the problem was wrong, but this is more of a line drawing problem than a problem in logic.
On the other hand the majority relies on the fact that the limits of the commerce clause are defined by precedent. With this view the Court cannot get close to what Justice Story stated and what the original intent was.
Scalia didn’t go to the promised land with his concurrence, but he took a big step in that direction in that he tied the doctrine back to the Constitution instead of leaving it hanging unattached.