My humble suggestions to what would have been the "Nightmare" versions of each level:
Alabastra: Mostly the same, but I would have had them save Vivi and Cobra on-screen.
Water 7: They start in W7, CP9 steals the Pluton blueprints, they go to Enies Lobby. Not sure if I would have Whitebeard there, tho.
Marineford: Blackbeard gets the Cube and defeats the Marines. Remnants of the Whitebeard Pirates are trapped there and need you to defeat him.
Dressrosa: Law actually does more with the Cube and takes over the country as King.