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Assuming that Holder is nominated and confirmed as A.G., then the partisan political background of Mr. Holder will detract somewhat from the appearance of legitimacy.
It's true that Holder was eminently qualified to be A.G. (and had already served briefly as acting A.G.) before Holder met Obama, but his becoming a political advisor to Obama changed Holder's position.
Holder's not a crony and not a hack but, still, he was a member of the Obama political campaign, and a more independent A.G. would have been preferable.
Of course, even if Obama picked Orrin Hatch as A.G., the right wing noise machine would still end up saying that any investigation or prosecution of Bush Administration officials (or of any Republicans) was partisan and illegitimate.
But still, since Obama has announced that he will have a bunch of Republicans at high levels, why wouldn't the A.G. be a logical spot for one? Or, even better, a logical spot for somebody who HASN'T been involved in partisan politics?