Many people guessed that Jean was the killer, which indicates to me that it had some rationale to it. To me, it made sense, although I agree with you that the Atom would have been a preferable killer. (I had guessed he was not when I saw a recent cover to JLAdventures, in which the Atom starred - seemed unlikely that a hero turned killer would appear in a kid's title.)
DC will not do anything to its top tier properties (which includes Luthor and the Joker), because they are the ones that make money through licensing. With this limitation, Meltzer did a decent job with the rest of them - he made the non- top tier Satellite era JLA (a revered Silver Age bunch) all complicit to a conspiracy of purposively giving a villain character brain damage, and, worse, made them attack Batman in order to preserve their grubby little secret.
To me, this has mean meaningful repercussions than destroying the Mulitverse in Crisis, because they are character repercussions. Green Arrow was still a good guy after Crisis. But now he's a little suspect - he helped brainwash Batman. Same goes for Zatanna and the rest of the crew. What they did was miserable and unheroic. There are now more shades of grey in the DCU than there has ever been.
My sole but significant criticism of the book remains the rape of Sue Dibny, which I still regard as completely unnecessary and written for the purposes of titilation. But I ahve been through this enough times already and won't belabour the point.
