I believe Watergate shows that the system did work. Particularly the Judiciary and the Congress, and ultimately an independent prosecutor working in the Executive Branch.
The transformation of the D.C. Circuit has been replicated in federal courts around the country. Obama has had two hundred and eighty judges confirmed, which represents about a third of the federal judiciary.
While abolishing judgeships and lower federal courts is a blunt tool and one whose use is warranted only in the most extreme of circumstances... it is one of many possibilities to check and balance the judiciary.
The framers of the Constitution were so clear in the federalist papers and elsewhere that they felt an independent judiciary was critical to the success of the nation.
Maintaining checks and balances on the power of the Judiciary Branch and the other two branches is vital to keep the form of government set up by our Founding Fathers.