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You probably don’t indict a sitting US Senator with the approval of the AG, unless of course you’re a special prosecutor. I’m not familiar with how PIS works, but let’s stipulate it works just the way you describe.

There’s a HUGE difference between the approval of pursuing an indictment and the prosecutors engaging in prosecutorial misconduct. Also, there’s no allegation that Gonzales (or anyone else for that matter in the Bush Administration) knew of the misconduct before, during or after the trial. It seems to me that you (and most of the MSM) is trying to give these prosecutors the benefit of the doubt that this wasn’t politically motivated because the prosecution occurred during Bush’s and Gonzalez’ tenure.

I believe nothing could be further from the truth. It is plausible, perhaps even likely, that these prosecutors acted unethically and even criminally precisely because if their political leanings, despite who their bosses may or may not have been.

Where does the buck stop in a Justice Department probe, indictment and prosecution?
Was Janet Reno responsible for Waco and for Elian Gonzales or were they the fault of politically motivated underlings?

If the Bush administration Justice Department had only prosecuted Senator Stevens, I might be able to give you the benefit of the doubt but what about Randy “Duke” Cunningham, Ohio Republican Congressman Bob Ney, Arizona Republican Congressman Rick Renzi, Jack Abramoff and Lewis “Scooter” Libby?
Can you name a top Democrat that they prosecuted under Ashcroft, Gonzales or Mukasey? Its the Attorney General’s responsiblity to make those calls.

"Was Janet Reno responsible for Waco and for Elian Gonzales or were they the fault of politically motivated underlings?

Well, the Waco and Gonzales cases are completely different from what's going on here. Waco and Gonzales were both green-lit from the White House; Of that, there is no question. The FBI didn't decide to assault the compound on their own, nor did ICE (INS at the time) decide to raid a house a kidnap a small child on their own. They were following orders. No one can claim that these prosecutors were following orders to act in an unethical or illegal manner. They did that all on their own.

As for who the DOJ prosecuted or did not prosecute during the Bush tenure, I'm not an expert. But I'd say that we're in some agreement here. Bush and his three AG's certainly weren't bashful about prosecuting Republicans. In fact, besides the Alabama Insurance case (I belive the guys name is Don Siegelman, but am not positive), I don't think that there were any high-profile cases that were brought against Dems or big Dem supporters. The William Jefferson case still hasn't made it to an indictment, let alone a trial.

But, some are claiming that this Stephens case can't be politically motivated because it happened under Bush's watch. With this, I disagree. I think that these prosecutors (career or otherwise) were looking to score political points during a contentious election year.