Another item that Madison proposed was making sure at least three of the liberties guaranteed in the Bill of Rights applied to all states.The proposed incorporation would have made clear that the states and the Federal guarantees were different, and might have made unnecessary the 14th Amendment's vesting of Federal Courts with such expansive powers. They might have been given only an additional power or two to oversee, rather than reordering the relationship between the states and the central government so completely. It is my sense that most of the serious tensions in American's politics come from the fact that the Federal courts impose one-sized-fits-all solutions on a nation that does not agree about fundamental questions of right.
“No State shall violate the equal rights of conscience, or the freedom of the press, or the trial by jury in criminal cases,” Madison said in the fifth part of his original Bill of Rights proposal.
The selective incorporation of parts of the Bill of Rights to the states didn’t happen until the early part of the 20th century as the Supreme Court interpreted the 14th Amendment’s Due Process Clause in a series of cases.
Madison also wanted to clearly spell out that each branch of government had clear, distinct roles.
“The powers delegated by this Constitution are appropriated to the departments to which they are respectively distributed: so that the Legislative Department shall never exercise the powers vested in the Executive or Judicial, nor the Executive exercise the powers vested in the Legislative or Judicial, nor the Judicial exercise the powers vested in the Legislative or Executive Departments,” he said in the last part of his proposed Bill of Rights.
The proposed clarity on the separation of powers would have been helpful, too, at least potentially. The Supreme Court understood the difference until Roosevelt intimidated them into yielding place. It's been a long fall since then.