Okay, when it comes to Arkham Knight, I do kind of have to agree with the assessment that it so radically changed the status quo that it's comparable to Mass Effect 3, though not to the same extent. Mostly, the game so wasted the premises of a United Batfamily defending Gotham, Jason Todd as an adversary with a mystery, United villains cooperating, Harley operating as the Joker's successor, Etc. Still, I can see options...
Option 1- Batman: Arkham Reborn. (Inspiration: Batman RIP and Batman Inc.)
Dick Grayson is the player character, as Batman. There's some ambiguity as to what his actual motivation is for wearing the suit at first, though it's soon solved when we find out that someone is deploying multiple "replacement Batmen" with lethal moves, kind of combining the evil Batman idea you guys have had with Morrison's 3 Batmen idea. Dick effectively manages to defeat them while also recruiting Jason and Tim into an alliance, with the former founding the Outlaws while the latter forms the Outsiders. Ultimately, it's revealed that Dick is working side by side with Bruce to create...Batman Inc. Jason and Tim both figured something was going on, but it's revealed to the audience when Catwoman tracks Bruce down while he's gearing up in another country (possible DLC fodder).
Most of the villains in the game are second generation (Emperor Penguin, Fright, female Scarface, the Jokerz street gang), or first gen villains coming to grips with a new world, like Two Face and Mad Hatter actually starting to heal and reform thanks to Bruce secretly taking over the running of a rebuilt Arkham, or Bane abdandining the conquest of Gotham while still being a villain. We find out that the Demon organization is in a 3-way civil war between Nyssa (generally accepted heir), Dusan (vengeful Ra's loyalists), and Talia (sneaky Leviathan). Damian, Cass and Steph are all introduced, and the final boss is one of the extremist Batmen abandoning their nominal heroism and becoming the Wrath.
Option 2- Batman: Arkham At Large. (Inspiration: Long Halloween, Dark Tomorrow, Heat, Mask of the Phantasm)
It's three or four years into Bruce's career, and it's the most brutally hot summer in Gotham City on record. Harvey Dent has just turned into Two-Face and Bruce is trying to track him down while simultaneously having to deal with both the Holiday serial killings and the final war between the old school mob and the freaks. Over the course of a single week, Batman and Robin have to deal with all of this, plus the return of Bruce's old flame Andrea Beaumont, who Dick immediately realizes has some ulterior motives.
The biggest thing about the game is that you use Detective Vision for all cases and you have to solve them to progress each plot thread. The Holiday killings tie into the Mob v Freaks war, and Bruce becomes aware for the first time that someone's screwing around in Arkham because Harvey clearly got worse; this mission has Joker's only appearance as he actually stays in his cell the entire time, though he's got Harley committing murders. About Andrea; here, she's a brunette with a familiar voice and accent, and you'll realize why after a side mission as Catwoman to steal some of her stuff triggers the final nights: Andrea Beaumont is Talia Al Ghul, and they capture Bruce in his own mansion and cave, so Catwoman and Robin have to realize as him for the fight against Ra's.