While Amanda Waller's most notable achievement is probably the creation of the Suicide Squad, that's certainly not the only way she's affected the larger DC Universe. In fact, Waller was actually responsible for creating the DC Animated Universe version of Terry McGinnis, who went on to become Batman Beyond's Dark Knight.
In Justice League Unlimited Season 2, Episode 13, "Epilogue," Terry discovers he's practically a clone of Batman and breaks into Waller's home to search for answers. After sharing his suspicions with her, Waller explains exactly what she did and why. As a woman of action, Waller has always been prepared to use any means necessary to safeguard national security. So, after acknowledging Batman as an asset, she created Project Batman Beyond to create the next Dark Knight in the event of Bruce Wayne's demise or retirement.
Waller’s methods have always been a bit crude, but had Project Batman Beyond gone completely according to plan, would have crossed ethical boundaries in horrifying ways. The plan required her to harvest DNA samples from Batman in order to obtain information on his genetic makeup. From there, the team used that information with technology from CADMUS to program nanobots that, when injected, were capable of rewriting a man’s reproductive material to match Bruce Wayne’s.
But Waller couldn’t just pick any man at random. For Project Batman Beyond to succeed, she needed to find a couple that was a close enough psychological match to Thomas and Martha Wayne. She found her subjects in Warren and Mary McGinnis. So, under the pretense of a simple flu shot, Warren was injected with the nanobots. About a year later, Terry was born, sharing half his DNA with Bruce.
However, that's not where Project Batman Beyond's machinations ended. In "Epilogue," Waller tells Terry, "When you’re making a Batman, genetics is only part of the story." Project Batman Beyond didn't aim to just copy Bruce's DNA. Instead, Waller wanted to recreate the circumstances that led to Bruce becoming Batman, meaning Warren and Mary had to die in front of Terry. While Waller had no qualms about traumatizing the young Terry, The Phantasm -- who was hired to kill the McGinnis couple -- backed out at the last minute, arguing murder would not honor Batman's legacy. Waller reluctantly agreed.
Project Batman Beyond was then abandoned, and the McGinnis family was left alone. However, Waller’s change of heart was all for naught, as Terry’s father was murdered anyway when he was a teenager. Warren's death ends up having the exact effect that Waller hoped and Terry becomes consumed by the desire to bring his father’s killers to justice, which causes him to take up the mantle of Batman and train with Bruce.
In the end, Project Batman Beyond may not have gone exactly as Waller planned, but she does deserve some major credit for creating the future's version of the Dark Knight.