JSA mentioned the "Darkseid Incident", no Hawks, no Batman, Barry is back, no Monitors, no New Gods, Darksied is dead, Aquaman is back, then the FC aftermath stories are later.
Because FC dealt with time anomalies and all sorts it's not left the world significantly different and it's difficult to explain how it affected the world. A little like Rock of Ages.
The thing is as well Final Crisis dealt a lot with characters who don't have monthlies, Checkmate, Rennie Montoya, The Atoms, New Gods/Darkseid, Monitors, Alpha Lanterns, Bludhaven, Uncle Sam & Freedom Fighters, the Flashs, SHADE, Frankenstein, Aquaman, then Morissons own creations for the series.
These characters don't have the books to show how their world is going on now - to me the problem is that while Morisson has done this huge event DC haven't supported it through their own titles.