Our Constitution, while admirable in many respects, has some deep flaws, especially the federal court structure. But given the flawed court structure, it has developed one very redeeming feature: the Incorporation Doctrine. Under this doctrine, said by the Supreme Court to be implied from the 14th Amendment clause requiring States to respect due process, the federal Bill of Rights is applied as a limitation on States. This doctrine has allowed federal courts to enforce many individual rights against state governments, which state courts have far less incentive to do, even though similar or the same rights are written into most state constitutions. Combined with the doctrine that the Bill of Rights means the same thing when applied to States as they do when applied against the federal government, (the Same-Scope Doctrine -- an assumption that on original meaning grounds is perhaps flawed), it has also given the federal courts far more incentive to enforce the Bill of Rights against the federal government itself.
A brief further explanation of the basic flaws in both federal and state courts are in order. These courts are selected by the legislatures and executive whose power they interpret. This gives a strong selection bias (similar to adverse selection in economics, but involving the choices of third parties). When on the bench, operational bias (analogous to moral hazard in economics) biases verdicts towards increasing both federal power and the rights of other parties as narrow exceptions to those powers in order to increase the number and importance of disputes, and thereby increase the importance of the federal courts. The same logic applies to state courts interpreting the powers of state legislatures and executives under state constitutions.
An example of selection bias at work: you will almost always see Senators ask judicial nominees their opinion on the Commerce Clause. To be approved, the nominee cannot declare an intention to overturn preposterous interpretation by which "commerce among the States" includes growing marijuana or wheat in your own backyard for your own consumption. If a nominee does not declare allegience to this legal monstrosity, which has vastly increased the power of the President and Senate, most Presidents and Senates will not allow him on the federal bench. (The occassional joker, like Justice Thomas, does slip past both the President and Senate, but it's very rare).
Before the Incorporation Doctrine and the same-scope assumption, federal courts rarely enforced the Bill of Rights against the federal government. They enforced the small handful of limitations on the States in the original Constitution far more zealously. The combination of selection and operational biases produces this result -- the federal courts want to inrease their influence by enforcing rights, but have to commit to Senators (and often the President) who select them to not enforce them strongly against federal legislative or executive acts. They don't need to commit to States -- the States are not a source of selection bias -- so they can exercise their power freely by enforcing rights against the States.
Thus the federal courts have always been eager to enforce individual rights against the States, but very reticent to do so against the federal government. The Incorporation Doctrine and the same-scope assumption cause the federal courts to enforce the Bill of Rights against the federal government, going against their selection bias, as a price they are willing to pay to enforce a larger set of rights against the States.
A much better solution for keeping governmental powers in check and rights protected would be to have federal courts interpret state constitutions, and set up a new super-federal court, selected completely independently of federal politicians, to interpret the U.S. Constitution. Until such radical modification, the Incorporation and Same-Scope doctrines are crucial to incentivizing federal courts to enforce the Bill of Rights today.