What's different is that prior to 2009, the Bush administration considered such 'enhanced interrogation' methods to be legal, and instructed intelligence agents accordingly. People have been pardoned for activities that they were assured were legal and ordered to carry out - a sticky moral situation to be sure, but courts decide issues of law rather than morality.
Since the change in 2009, nobody can say they thought things like waterboarding were legal, and if some field agent were to carry it out s/he would have no defense available in law.
I don't want to turn this intoa Republican/Democrat political issue, but to pretend the two administrations are the same on this issue is just not credible and does not make for a constructive discussion. You can find plenty to criticize about the incumbent administration without needing to invent more.