Here's my idea, a combination of Batman Beyond and Young Justice:
Synopsis: Twenty five years ago there was a Great Crisis, in which the combined forces of heroes and villains fought valiantly to repel the forces of Darkseid. Though the champions of earth prevailed, all were killed, save Batman. Shortly after this tragedy the Government developed Project Cadmus. Under the guise of a government funded fertility program, Cadmus attempted to recreate their fallen heroes by implanting their genetic material (the metagene) into relatives undergoing fertility treatments. The project had three (and perhaps four) successes:
Bruce Wayne continued his role as Gothams protector, but eventually retired to live out his life alone in Wayne Manor. At the urging of Gotham University, Wayne eventually agreed to have assistance in the form of Terry McGinness, a former Navy Seal recently enrolled at the school. At the same time, the Government has determined the clones to be too dangerous (and valuable) out on their own, and sent its Amazo robot to forcibly collect the results of Project Cadmus: Iris West, Connor Kent and Virgil Hawkins. With the assistance of a hospitalized Amanda Walker, Terry and Bruce must combine forces to free the clones from Cadmus. And perhaps, start a new Justice League.