How can extreme prosecutorial power be checked?

Thanks to this post at the WSJ Law Blog, I see that Judge Lewis Kaplan is talking about the need to check prosecutorial power in corporate crime investigations.  This Wall Street Journal article provides these details:

The federal judge in the case involving allegedly fraudulent tax shelters marketed by KPMG LLP said it may be time to re-examine laws governing corporate criminal liability and the tactics used by prosecutors to investigate those cases. 

US District Judge Lewis A. Kaplan, speaking at a National Association of Criminal Defense Lawyers seminar, said the KPMG case and others, such as the government’s prosecution of Adelphia Communications Corp. executives, raise questions about the government’s practice of using the threat of criminal prosecution of companies in order to gain leverage in investigations of alleged wrongdoing by company employees.

He said the laws appear to give expansive power to prosecutors, lessening the oversight of courts and juries, at the expense of the constitutional rights of those accused. “I question whether placing virtually unchecked power in the hands of any branch of government” is the right thing, Judge Kaplan said.

Of course, as many know — especially those in places like Durham and Jena or those involved in cases like the border agents and Genarlow Wilson — issues of extreme prosecutorial power and the potential for abuse are not confined to corporate settings.  Especially now that prosecutors can often credibly threaten decades in prison even for first offenders if they risk going to trial (and then can get sentence enhancements even for acquitted conduct), the potency of prosecutorial threats cannot be overstated.

Indeed, I became of fan of Apprendi and Blakely in part because I was hopeful the Supreme Court was coming to appreciate the dire need for new constitutional doctrines to check extreme prosecutorial power.  Unfortunately, as the Booker remedy and many lower court rulings after Booker highlight, it is very hard to convince judges just how important it is to expand constitutional doctrines and procedural rights to restore balance in the operation of the modern criminal justice system.

In short, I strongly believe greater checks on prosecutorial power are desperately needed.  But I am quite unsure how to effectively engineer and sustain greater checks on prosecutorial power, especially in our persistent tough-on-crime political climate. 

Any good ideas, dear readers?