The Department of Justice has suffered from a bruised reputation in recent years following a host of controversies during the current administration.
One of the major criticisms was that it hired and fired U.S. Attorneys based on political leanings and ideology rather than competence and experience.
Former U.S. Attorney Tom Heffelfinger served under both Bush administrations but left for private practice years ago while working under George W. Bush.
He did not know as he left, but he was on a list of 30 U.S. Attorneys to be fired, Heffelfinger said.
In May of last year, an aide to then-Attorney General Alberto Gonzales told Congress that Heffelfinger was on the list because he spent too much time fighting crime on Indian reservations.
Heffelfinger said Barack Obama needs to choose a strong leader in an attorney general and one who's worked in the justice department.
"Bringing somebody from the outside as we saw with General Gonzales simply was a recipe for disaster. You have to hold the job with a fundamental understanding of what the role of a prosecutor is, what the role of the department of justice is, and it's role vis a vis the president," Heffelfinger said.
Former U.S. Attorney B. Todd Jones, a Clinton-appointee, said Obama inherits a Justice Department facing many challenges, including low moral and a higher than average number of open positions at senior levels.
"With all of those factors in place, too, we have a global war on terrorism. And this is a transition that's particularly important for the incoming and outgoing administrations to have a whole heck of a lot more communication in doing the transition because DOJ like the Department of Defense is on the front lines in a number of ways with national security issues," Jones said.
One of those national security issues facing the administration, Jones said, is what to do about those being held at Guantanamo Bay as enemy combatants.
"A Guantanamo wind-down is probably in the top three priorities for what you're going to hear after the personnel issues are fleshed out for the attorney general because there is no doubt that they are going to wind down Guantanamo as quickly as they can," Jones said.
Heffelfinger said of the lingering debates in ending Guantanamo is whether the U.S. should use the largely open criminal justice system to try suspected terrorists.
There have been published reports that President-elect Barack Obama is considering an alternative called National Security Courts, which would specialize in trying suspected terrorists.
"I just don't believe that the nature of the evidence generated in these cases and the unique security interests involved in a prosecutions of that type is amenable to those types of procedures that we use in an average criminal case. We're going to have to find something that's a hybrid between the current system and a full public trial," Heffelfinger said.
Heffelfinger said in addition to terrorism, he expects the justice system will make prosecuting white collar crime a higher priority than the last administration.
"And I don't see how it cannot be. How can Congress put together a bailout package like this without coming back in January with a whole bunch of more money for assistant U.S. Attorneys, FBI agents and the like? And quite frankly, it's going to be helpful," Heffelfinger said.
B. Todd Jones agreed.
"Whether its mortgage fraud, securities fraud, I think you've seen some things that have happened recently with a local company here, a billion-dollar fraud. And those are the kinds of cases that the U.S. Attorney's office is uniquely positioned to do because of the investigative tools like a grand jury," Jones said.
Those reportedly on Obama's short list for Attorney General include: former Deputy Attorney General Eric Holder; Arizona Gov. Janet Napolitano; and Rep. Artur Davis, an Alabama Democrat and member of House Judiciary Committee.