Missed this discussion the first time around! But I'm thinking Jeff Vandermeer books could be great apocalyptic systems novels. They usually involve individuals trying to navigate very shadowy, very large governmental or underworld type organizations, all while attempting to unravel a mystery or disappearance. His books also most certainly involve the apocalypse or apocalyptic type scenarios... in The Southern Reach Trilogy, Borne, and Veniss Underground, something completely transformative has happened to the world (or the transformation is underway) in all of those books.
I'm also waiting for someone to write the great systems novel uniting politics, the global drug trade, and soccer hooliganism. Could it be you, Max? Related reading: