Rather than rebuild an entire game that is already solid; I'd like to see additional dlc in the form of new stories.
Example. Regardless of the ending Reid returns to his family home. Dead citizens are replaced with new characters who act essentially the same had the originals not died. New investigations, a new main story line, new multiple endings.
If Lady Ashbury is still alive perhaps she can return as well, with both living apart in their respective homes or together. Perhaps we can choose to play one or the either with each dlc.
In short, nothing changes as far as the locations or the game mechanics. Just new stories and new citizens sprinkled in from dlc to dlc when previous citizens die.
I would also suggest when a district is "lost" rather than kill everyone off just make them unavailable as the guard locks the district down and roams those streets in heavy numbers. At least until the next dlc.