Bruce Wayne pulled off some real miracles as Batman, locking up major criminals from his rogue's gallery. Many of his old villains don't appear in their ancient form in Batman Beyond… which is a testament to Bruce's effectiveness.
We DO see the heirs of those different legacies, such as the Jokerz. Though inspired by the Joker, they're more of a semi-dangerous nuisance than a city-ending threat.
But another heir we see is Terry McGuiness, the heir to the title of Batman… the seeds of which (some spoilers) were planted before Bruce retired. Terry wouldn't exist as a person or as Batman had Bruce's original crusade not succeeded in the eyes of Terry himself and Amanda Waller. Both Terry and Amanda, in their own way, looked up to what Batman represented and what he could do, and when opportunities came to further that legacy, they jumped at it.
Though dangerous as a city during Bruce's forced retirement from being Batman, Gotham moved on. It got more extensive, and as Bruce slowly gave up on trying to manage the state of affairs in the city (as is indicated by his role in Wayne-Powers and lack of connection to his former partners), the natural decline of Gotham continued.
But it's interesting to note that it wasn't all in vain. We don't HEAR ABOUT or SEE ANY supervillains that exist before Terry takes on the mantle. Terry never talks about growing up during any villain's reign of terror or that his part of Gotham was controlled by a territorial crime boss, like Two-Face or Penguin. Most of Batman's rogue's gallery and most organized crime were defeated.
For all intents and purposes… Batman did clean up the parts of Gotham that the police couldn't handle. Many of his old villains who survived that era only make it into Terry's rogue's gallery because of some very tricky science… and weren't active until Terry took the mantle up or stayed out of Gotham.
And let's not forget that there's one other heir that needs to be talked about:
Barbara Gordon, the police commissioner.
Her long and arduous tenure as the police commissioner is not only due to her father's influence but Bruce's as well. And in many ways, I think what she learned from him helped her to keep Gotham clear of the psychos who could eventually become supervillains or lock up the would-be world-beaters that did arise between Bruce's retirement and the start of Batman Beyond.
In the first episode, Bruce's first instruction to Terry is for him to bring the evidence concerning Wayne-Powers to Barbara… Terry is reluctant due to his history with the cops, but it shows that Bruce has a lot of faith in his former protégé and how she handles things. Well… at least until new opportunities present themselves in the form of Terry.
It was not all in vain. Terry didn't really grow up in a time where the Joker was terrorizing the city by poisoning fish or holding the city hostage with God-only-knows what kind of scheme… or the Riddler was playing death games with citizens, or Clay face could be walking around as anyone. The Gotham Terry grew up in had crime, like most major cities, and corruption. Still, since there's no significant supervillain presence or omnipresent mob family in control of Gotham, I think Bruce did an excellent job of clearing it out before retiring.
