Separation of Powers or Duplication of Powers?
The Bush administration has been intent on showing how hollow the separation of powers really is. The problem is the kind of power that each branch has. All of the physical power belongs to the executive branch. They have the guns and the keys to the jail and the PIN for the nation's treasury. The other two branches only have the soft power to give or withhold approval. They only have as much power as the executive branch is willing to grant them by caring what they say.
The Bush administration hasn't blatantly defied Congress or the courts yet. They still claim that they're respecting the other branches' authority, even though the legal fig leaves they use to create the appearance of legitimacy have become more and more caterpillar-chewed. We're in a situation now where Bush can use signing statements to rewrite laws as he pleases, and attempts to hold him accountable to Congress (e.g. in the Justice Department firing scandal) have ground to a halt because the only way to compel the executive branch's testimony is to have it prosecuted by the executive branch.
But if unitary power is no good, and separation of powers is no good (because it just collapses into unitary power as soon as the right branch gets a leader with big enough gonads), what's the solution? It seems to me we should consider some form of duplication of powers. That is, each branch of government will have the same set of powers, so they can directly check each other rather than writing sternly worded letters that another branch can just toss in the circular file. I don't know quite what a duplication of powers system would look like, but it seems to be an avenue worth exploring. In other words, eventually, President Bush (or President Romney, or President Clinton) whill essentially say to the other branches "oh yeah? You and what army?" So perhaps the solution is to give them their own armies.