The continuity of counter-terrorism policy from Bush to Obama was an ongoing theme of a conference called "Law, Security and Liberty after 9/11" at the Harvard Law School and featured John Brennan (on the record and taking questions) and a bevy of elite national security lawyers on panels.

It's safe to say that all the former Obama lawyers took exception to the notion that there was continuity and most of the former Bush lawyers insisted that there was. Jack Goldsmith went so far as to quote Glenn Greenwald to make his case.

Charlie Savage gave the closing keynote and he tried to put this in a larger framework. From his perspective, the difference between Bush and Obama was not so much outcome but process. While the Bush policies (before the Jack Goldsmith revolt) were based on the theories of the unitary executive and the commander and chief's war time authorities, the Obama administration has dismantled those justifications and put them back together with what they believe is a rigid adherence to the rule of law. That they come out in the same place is just a coincidence.

That line of reasoning is parallel to yours. A focus on who we really went to war with on 9/11 is part of that whole shift to sound footings for the various policies.

Not to pimp my own work, but I wrote up the conference here:

http://www.cctvcambridge.org/LawSecurityandLiberty

Charlie Savage has expanded his keynote to a $.99 Kindle single here:

http://www.amazon.com/Power-Wars-Unmasking-Deliberations-ebook/dp/B005OTY468/ref=sr_1_1?ie=UTF8&qid=1317497820&sr=8-1