I had commented that I would make Star Wars 1313 a while ago. For a non-SW suggestion, I would suggest Batman: Arkham Knight.
The Arkham Knight would now be an older Damian Wayne leading the League of Shadows. He would be hunting down Batman to avenge Talia's death.
The armored Batsuit would be replaced with the Batman Beyond suit. I also would have added to the gliding mechanics through the use of the Beyond suit's jet-boots.
The story would take inspiration from The Dark Knight Returns since it would have an older Bruce come out of retirement for one last night. This would allow for a satisfying conclusion to the series as it would be a subtle nod to this being the last game in the Arkham series. This would add more emotional weight to the story.
The Scarecrow would be one of the main villains, but not the main villains. While he is an interesting villain with a lot of setup throughout Arkham City, I don't think he can carry the game by himself.
I would also bring back Hush as one of the villains so that he could take over Wayne Enterprises, but in a more interesting way than just trying to steal money.
The Joker segments wouldn't start as early into the game. I'm okay with him being involved, but have it as the Scarecrow gas driving Batman insane rather than literally turning into the Joker. Use it as a way for the player to be unsure about Batman since he would become an unreliable narrator/POV. I would keep some of the Joker scenes (The Killing Joke/Jason flashbacks).
I would have the game end with Batman dying and/or officially giving the role to Azrael so that AK would wrap up that plot thread a bit better.
Nightwing's appearance and story would be similar to how it plays out. Unfortunately, they didn't do much with him in the previous games.
Tim would be a lot less of a beta male. His only job in AK is to get captured and whine to/about Batman.
Oracle was fine, I liked her portrayal in AK. I would have had her kidnapping happen later in the game, though.
Jason coming back from the dead would have been a side story that emulated the Red Hood story. It would have been a nice diversion from the main story.
That's all I have for story ideas at the moment, so I'll leave one more major change: Only keep 25% or less of the Batmobile sections. I want to play as BATMAN, not the friggin car.
Sorry for my long post, I've had many thoughts regarding what I wanted from this game versus what we actually got. It has a lot of good elements (the combat, visuals, voice acting, alternate suits, etc.), but the missteps are very unfortunate.