I disagree that 'Luthor as President' was dismantled badly by Loeb. It tied with what Johns and Didio wanted at the time, to return Luthor to the 'mad scientist' he was before Byrne's idea of making him a corporate entity. Plus, Lex as President is the same as Osborn in charge of HAMMER - at the end of the day, there's always going to be one little flaw that will destroy whatever regime they have. For Lex, it's Superman, and he's obsessed with destroying him, and for Osborn, he's just plain nutty and hates superhumans. Both are destined to fail because of those flaws.
And the Metallo = Wayne Murdered plotline was indeed resolved as a ruse.