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I am posting this without having read the 160 or so letters that came before, so feel free to disregard if what I'm saying is redundant or superfluous.
I don't think Holder arguing that detainees were not prisoners of war as defined by Geneva is a big deal. There are multiple classifications within the treaty, and prisoners of war have to meet qualifications that suspected terrorists simply can not (weapon displayed openly, wearing a uniform, etc.). They are still entitled to rights under Geneva as enemy combatants (I believe under common article 3 as Glenn mentioned). What the administration was attempting to do was classify suspected terrorists as "unlawful enemy combatants," and then argue that this classification forecloses any and all rights. I don't think Holder ever supported that position.
Prisoners of war under Geneva may not be interrogated at all, beyond name rank and serial number. Any president would want the ability to question suspected terrorists, although I hope most presidents would do so humanely and within the bounds of law. I think the problem of international terrorism could much more effectively be battled without military intervention at all, simply through cooperation among global law enforcement authorities, but of course the Bush administration has set us back a few decades on that front. Think of what we could have accomplished with the goodwill we had after 9/11.
I also don't think Holder arguing for detention of suspected terrorists until the end of the "war" in 2002 is troubling. At that point in time, it may have been reasonable (although perhaps naive) to say that the "war" would end after Bin Laden was killed or captured. Now that most people are aware that this "war on terror" will probably continue until we decide on a better name, the idea of detaining until it ends is ridiculous. The eventual realization of SCOTUS that detainees in Guantanamo were in a perpetual state of legal limbo has been suggested as a factor in the Court changing its mind on cert in Boumediene, and deciding as they did.
(Cert was originally denied to Boumediene. Either Stevens or Kennedy or both changed their mind and cert was granted on a rehearing of some sort - the procedural details are fuzzy for me)