In reality, I doubt there's much for Hancock and the BCS to fear. The DoJ already questioned the NCAA last month about cfb's post season, but they were able to (happily, I'm sure) pass the buck. So what we have is a pro-playoff element vs. the BCS. And while the BCS' biggest motivator is undoubtedly profit, they at least have a legal defense:
"The BCS was carefully created with antitrust laws in mind, and I am confident that it is fully compliant with those laws. It has improved competition by delivering a national championship game between the two top-ranked teams, which only rarely existed before the BCS. It has also dramatically increased access to top-tier bowl games for schools from non-AQ conferences. I look forward to a conversation with the attorneys at the Justice Department.”
This is all true. We might not like computer-based input, but we do get 1 vs. 2. And, the refined non-AQ clause and the fact they revisit who qualifies to, well, qualify, could be enough to protect them. BYU got their title back in the day - and they were the only undefeated, untied team and no national power had just one loss. In the last seven years, if Boise State would have ever done under those circumstances, they probably would have been national champs - thanks, oddly enough, to the BCS system allowing a small school from the WAC to play in a major bowl despite the fact they cannot sell out their own home stadium. There's your access and opportunity.
Despite what the constituents of the people who pushed this investigation hope, this will probably not become the long dreamed of referendum on a playoff system. The fact of the matter is no different now than it has been since 1998: when the money's right, they'll be a playoff. Until then, the BCS reps and AQ conferences and university presidents will still hide behind things like academic concerns, extra games, operating costs, etc.
Personally, I go back and forth between the bowl system and a playoff. I honestly spend more time day dreaming about super conferences and realignment. What I do know is that what i think means ZERO on what's going to change or remain the same about our post-season system. Kind like this DoJ inquiry...