Someone ought to ask Breyer if he's ever heard of the three COMPETING branches of government. When one abuses its power, then it is subject to checks and balances. If he wants the courts to remain independent, then they should stop abusing their power.
You said it... it's the "checks and balances," stupid.
The fact of the matter is that the Founding Fathers intentionally created the judiciary with less power than the executive or legislative branches. There is no provision in the Constitution for the courts to determine what is and isn't constitutional, the courts seized this power with Marbury v. Madison. Over the past two centuries, they have become more brazen with their power grabs, and with the exception of Andrew Jackson, nobody has ever stood up to them.
We recently had a situation during the Schiavo matter (and how any of us feel about that controversy is irrelevant here) where a judge openly ignored a Congressional subpoena, and Congress did nothing. In my opinion, there have been many instances where Congress and/or the President should have chosen to ignore a court ruling they felt was unlawful, yet they never do. Until the other branches of government decide to reassert their authority, the judiciary will continue it's tyranny.