This would be inevitable, to say the least.
For one thing, it's a Batman game, not a Justice League game. While it would probably be meant to bring up hype for the inevitable Justice League movie, it would also be stupid, if not for the reason that Batman is perhaps the most 'real' of the superheroes, and the games show that.
Except that part.
Now, I'm just a huge Batman fan, so it's not my place to say, (yes it is, fucker) but I want Rocksteady to just outdo Arkham City at every turn. How? Well, I'll tell you.
Number 1 - Keep the Joker Dead
It's already been established that Mark Hamill isn't doing the voice of the Joker anymore. It's understandable, seeing as how it's been thirty two years since the event that drove him insane, and now he's off to graze in less-fatherly pastures.
I also dislike Brent Spiner voicing the Joker. Makes me sick.
So imagine that Rocksteady has made Batman: Arkham State. All of Gotham State is a prison, and Governor Charles D. Dumfuq III has made the state a huge prison. Batman is still on patrol, and suddenly word gets out that the Black Mask is planning on conquering Arkham State and burn down the fields of Pennsylvania. In addition, Harley Quinn is still torn up about the Joker's death and is waging all-out war on Black Mask's crime empire. Like Arkham City, right? Yes, but it also gives time for new characters to develop, not just the Joker and some other minor character development. We could see some lesser-known villains who may or may not have made cameos, and they can have good roles. Other villains who had small roles - the Riddler comes to mind - in the previous installments can be major antagonists in the sequel. Also, there's lots of room left open for Hush being a major enemy, as in Arkham City, he donned Bruce Wayne's appearance.
Another good thing is Batman's character development. In Asylum, Batman was trapped by the Joker and forced to use his wits (and an emergency Batcave) to fight a guerilla war and win it in a single Bat-night. He developed a little, mainly how he was driven to the edge by the Joker.
"They trashed by God-Damned-Batmobile! NOOOOOO!"
In Arkham City, Batman was in a similar situation, but was fighting Hugo Strange and Ra's al Ghul. It upped the situation, and also made Batman more cautious since they both know (or, knew, rather) that he is actually Bruce Wayne, and might've used it against him. He also is a bit more driven to the edge, rather early on as well, but he does have enough Bat-level-headedness to see the opportunities he gets; for example, he uses Bane to track down Titan samples so that he can destroy them, and he saves Mr. Freeze's wife Nora, after she is captured by the Joker's thugs. And at the end, (seen more during Harley Quinn's Revenge) Batman has become unstable due to the Joker's death, as has Harley. Now he's trying to stop working with Robin, and he's even more isolated than before.
Now, we can see a development in Batman, and how he has coped. Maybe the DCAU route, where he cuts off Robin and Oracle from helping him. We may also see a Dark Knight Returns/Rises scenario, where Wayne has hung up the Bat-cowl and has been a recluse for some time.
2 - Keep the Justice League Away
Now, don't get me wrong, the Justice League are cool dudes.
Well, most of the time anyways...
But in a Batman game, I want to see Batman kicking ass and taking Bat-names. Batman.
If I wanted to be Superman or Wonder Woman, (which I wouldn't, because I want to be Batman) then I'll buy a Justice League game. But those don't exist, and if they do they probably suck. Nevertheless, I'd pick Batman anyways, because he's Batman.
Now, why is it such a bad idea, other than it being completely stupid? Well, it takes realism out of it.
I know, I know, a man dressing like a Bat isn't that realistic. But it's the closest to being real. Which makes it relatable. Yeah, we all wish we could move planets like Superman, or even eat them like Galacticus.
But Batman is just a man. Albeit, a man with billions of dollars and a mansion, but a man nonetheless. He has willpower, and knows martial arts. That's it. Even the Power Rangers, with their kickass ninja skills, had magical powers. Though, the Zords are kinda like the Bat-vehicles. And Zordon seems a lot like Alfred. Coincidence?! Probably.
Anyways, why we like Batman is because he's relatable to regular humans, as opposed to Superman, who is a god-damned alien with some fucked up anatomy that makes him super strong in yellow Sun. In a few thousand years, though, the Sun will be red, and that'll fuck him up a bit.
3 - More Intense
Now, don't get me wrong; the games are damn intense, and I know that the sequel will be too. But, I want more.
For one, Hush is out there, and he has Bruce Wayne's face. The possibilities are endless. For one, Hush could kill someone and frame Wayne. But that's not all. A huge confrontation with Hush would be very symbolic; Batman fighting Bruce Wayne. A mere appearance, yes, but it could mean that Batman and Bruce Wayne find themselves drifting apart, with the being they inhabit trying to balance them out, much like in the Dark Knight Rises.
Second, there's still Scarecrow, and boy I cannot wait for this. Scarecrow was supposedly killed by Killer Croc in Asylum, but his mask, as well as a boat containing shipments of bugs to "Dr. Crane" are in Arkham City, as are other hints I'm too lazy to point out. If Scarecrow returns, it'll be big. He'll be pissed at Batman for nearly killing him in Asylum, and it's stated in the Arkhamverse that he's probably very sane - just pure fucking evil. That's good enough to make him a damned effective and powerful villain, being able to drive Batman to the limit more than Ra's al Ghul or the Joker ever could.
Third, in the DLC Harley Quinn's Revenge, Commissioner Gordon says, in the beginning, "When this mess is all cleared up, we need to talk about that other problem, remember?" Other problem? Holy shit, what could that mean? Now, it could just mean the Joker's death, and Gordon knows something is up. But...
My theory is that perhaps the public thinks Batman killed the Joker, and also Hugo Strange. With them dead, and only Batman, Robin, and Alfred knowing this, the public could brand Batman a killer. Gordon would defend Batman, of course, but in the end, it could mean Gordon being forced to 'retire' and a new commissioner taking over and ordering a manhunt for Batman. That would mean that while Batman is fighting a Hush/Harley Quinn/Black Mask/Riddler/Scarecrow plot, he would also need to do it without the GCPD, and while avoiding them hunting him. Only adding to the sheer badassery, it would probably end with Batman being a hero, and maybe faking his death, a la the Dark Knight Rises.
Other Shit
Obviously there's more; lots more. Is Harley Quinn really pregnant? Maybe, but probably not. It'd be cool to see an older, Dark Knight Returns-style Batman fighting the Joker's son, but that probably won't happen. Either way, there are lots of stuff that needs to happen, but I hope Rocksteady will pull it off good.