I disagree. I think the fundamental problem is that we didn't step up and make whatever necessary amendments were needed if that original grant of power needed to be modified.
The fundamental problem is that we got too damned lazy to fight the politicians and make them do it right, and they let them turn it into an open-ended grant of power.
What Story warned against is exactly what happened, and we're facing the prospect of civil war to get it remedied and the longer it goes on the worse it's going to be when if comes down to it.
At best, it can be said that by implication, in the seldom expressed understanding of the Framers of the Constitution, and in early commerce clause cases, purely intrastate commerce was regarded as beyond the scope of the federal commerce clause power. In practice, the distinction between intrastate and interstate commerce has changed according to how they are defined and the circumstances of the era.
If not for the medical marijuana issue, I doubt that the federal commerce clause would be of much interest to anyone except legal scholars and a handful of practitioners. It is not the stuff that makes for civil wars.