The Watergate investigation created a generation of Republicans hell-bent on revenge. They considered it a witch hunt that went far beyond whatever crimes committed. Many of the people on the Republican side who pushed the initial Travelgate and Whitewater investigations were dedicated Nixonians who saw Bill Clinton as the punching bag on which they could get even for the crucifixion of Richard Nixon. Lucianne Goldberg, who put Linda Tripp up to trapping Monica Lewinsky was and old Nixon Dirty Trickster. Dick Cheney got his start in the Nixon administration and still resents that Nixon was forced to resign.
Everyone in Washington knows that if Bush and Cheney were to be investigated, impeached or convicted for any of a number of possible impeachable offenses, the resulting division in the country would divide the American people for 2 or 3 generations to come.
This is part of the reason Pelosi has steadfastly declared impeachment off the table: If it were on the table now, nothing else would be. And the public could easily end up siding with the Republicans, even though it's patently obvious that Cheney, if not Bush, has committed more than one "impeachable offense." Would 51% of the House vote to impeach? Possibly not. If they did, would 67% of the Senate vote to convict? Probably not.
Faced with choice between allowing a demoralizing prosecution of the previous regime or crafting a positive upbeat agenda of his own, I think Obama would opt for presidential pardon or declaring, as Pelosi did, that investigation and prosecution are off the table. I can't see him allowing his first 100 days to be co-opted by revenge.