Note: This is being specifically written as to what I'd like Arkham 3 to be like, just what I'd like to see as an installment in the series.
When I first found out that one of the pre-order bonuses for Arkham City was the Batman Beyond skin, I was very excited to see a little bit of fan service for a series that was well received for continuing the legacy of the dark knight that was started in Batman The Animated Series. Batman Beyond tool the dark knight mantle and put it in the hands of a new owner, the young Terry Mcginnis, who was being mentored by the previous and original Batman, Bruce Wayne. While the series was well received, it sadly only had a short life span of three seasons, from 1999 to 2001, being put on hold for production of The Justice League, despite plans for a fourth season, which has, to this day, never seen the light of day.
Batman Beyond was darker, than it's predecessor, with in the opening episode Batman having a heart attack mid fight and using a gun against his opponent, something that this rendition of the dark knight would never do, forcing him to drop the mantle of the bat. The next shocking occurrence is when Terry's father is murder by gang members impersonating The Joker, aptly named The Jokerz, since the original Clown Prince of Crime has been dead for many years in this continuity. Many of the themes of the series included emotions, and the stress on Terry as lead a double life as himself and Batman, and Bruce, dealing with the years of mental stress he had placed under while Batman, and the stress caused by passing the burden onto a much younger "replacement".
Over the three seasons, the new Batman built up his own Rogues gallery, matching the one of the previous dark knight, including Blight, Inque, an enhanced Mr Freeze, Shriek and even the Joker, resurrected in the body of Robin Tim Drake. And with much of the current Dark Knights rogue gallery exhausted in Arkham City, wouldn't be a good idea to use these enemies?
Picture the scene; Arkham 3 sees Batman (Bruce Wayne) fighting off the last of his rogues gallery, including Black Mask, Penguin, Mr Freeze etc who are all attempting to take over Gotham, eventually, after defeating each and everyone, he is reminded that Harley Quinn is pregnant with the baby of the Joker. Fearful of what the child might become, he goes after her, only being stopped when Harley Quinn gives birth, and, the first member of who would become the Jokerz, kills Robin, prompting Batman to drop the mantle of the bat after he failed to save his own.
Boom, fast forward a couple decades and a Mr Terry McGinnis is now the bat in his lean, skin tight spandex suit, and he has picked up the trail of Joker Jr, apparently taking over the Jokerz. Of course, with the return of the heir of the Jokers empire, this prompts many of the original Batman's villains to make a return, including Robin, who's corpse got dropped in a lazarus pit, turning him into The Red Hood, and the current Batman's villains, all to try and take Gotham.
Imagine it, gliding through the neon streets, in the cyber punk distopian city, fueled by gang warfare, and you, the Dark Knight, are the only hope that this city has, and now it's up to you to save Gotham one final time. Imagine a crossover of Batman Beyond Return of the Joker, Batman Under the Red Hood and Batman Arkham City all rolled into one. That's what I want the last entry in this series to be. Hell, you could even split the series into two trilogies, the first three being Arkham Asylum, Arkham City and Arkham 3, where you play as old Brucie boy, while in Arkham 4, 5 & 6, you play as Terry. I wouldn't complain. And maybe the restored faith in the Batman Beyond brand would force Warner Bros to contemplate that Batman Beyond movie they've put on hold, and even that fourth season.