The deluxe editions should have collected it proper.  It wasn't Grant Morrison's JLA: The Deluxe Edition, it was simply JLA: The Deluxe Edition.  They had a perfect opportunity to re-package the 19 JLA tpb's into 9 or 10 deluxe hardcovers.  Obviously the reversal and inclusion of skipped issues in the tpb's is an acknowledgement of their original bad judgement.