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The problem with investigating and prosecuting the last administration is pragmatic, not principled. If the outgoing administration is going to be jailed after they cede power, they may refuse to leave office.
Look at the power the incumbent administration has, and imagine it in the hands of the other party, without a safe way to leave office and retire to private life. If orderly transfer of power becomes impossible, if by leaving office President Bush is going to prison or signing his death warrant, he will refuse. Anybody would, for self-preservation alone, and then we have civil war. If the stakes are too high to leave office peacefully, no one will. This has happened before, in miniature, when President Andrew Johnson tried to fire Secretary of War Stanton and was impeached for it by Stanton's supporters, only escaping by 1 vote.
It's like being the highest ranking military officer in a third world country. You might not want to be in charge, but if the party that's elected is coming for you, your soldiers, and your family, it's self-defense to take over in a military coup d'etat (See Pinochet).
An investigation and prosecution of President Bush and Vice-President Cheney, unless done with the promise of amnesty for participation (even then I'm skeptical), is a very bad idea for the future of the republic.
