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.
As near as I can tell all that does is let them keep right on using the commerce clause to destroy the boundaries between the state and local govenments while arguing they're actually complying with the original intent of power while doing it.
Even this seems to pay lip service to that idea by only going back to 1937.