It's debatable whether this is a "fundamental" flaw, but the American Consitution is basically a set of procedural rules of the game. Civil rights are an afterthought.
Most modern constitutions also need all the procedures, of course, but they put certain "inalienable rights" square in the middle of it all. The procedures are merely there to support those rights.
The assumption of the time was that it was common-sense that the Constitution was a whitelist, not a blacklist. There was pushback against having an enumerated Bill of Rights because then there would be a whitelist of rights, and the Founders feared this would mean that they'd miss something and in the future their government would become oppressive.
Most modern constitutions also need all the procedures, of course, but they put certain "inalienable rights" square in the middle of it all. The procedures are merely there to support those rights.
Different times, different mindset.