While I like the different take on the DC universe, they really need to dial back on Batman being the great savior.
Batman talks down to Superman and the Regime, saying that it isn't their place to lead the entire world. Meanwhile, after merging with Luthor Corp, Wayne Industries is probably the biggest corporation in the world and Bruce Wayne is personally spearheading the reconstruction of the planet and guiding world councils on what to do. The irony of this is never brought up.
Secondly, Batman has constructed Brother Eye in this universe and has once again kept it secret from the world. In the mainstream comics, Batman's construction of a secret satellite (a re-imagining of the satellite that empowers OMAC, who would be a cool choice for a DLC character) that monitors and takes out supers was shown to be an awful idea stemming from his most paranoid period (thanks to Identity Crisis). Here, it's brushed aside as being necessary and not once is he reprimanded when it is immediately hijacked by Brainiac to expedite his conquest.
His disregard for the "circle of trust" in the beginning and his notion of him putting Superman behind bars is also kind of dumb, because if it wasn't for another universe's Justice League, especially their SUPERMAN, he'd never been able to stop the regime.
Batman is my favorite superhero and always has been since I was a kid. I love him, but it cheapens the character to make him the infallible cynic who will never bend and is always the best. They humanized Superman more in this game, despite his saturday morning villain routine in the last game, I just wished they would have done the same for Batman.
I would also like to know more about this universe's history of Batman. Superman's is really unique as he was completely untested. Luthor was his friend and only opposed him after the regime, he only heard of Brainiac and is only just now facing him, it's interesting to see how little hardships he faced before the Joker blowing up Metropolis with Lois and their child just instantly broke him. The only thing we now about Batman is that at least Dick, Jason, and Damien were Robins, but not much else.
Comics, my friend. The Injustice series goes into a lot of Batman's reasoning, methods, history, and experiences. And you better believe they call out his hypocrisy time and time again there.
The Superman of this universe is very untested, while this is a Batman that has had all four Robins (Tim's locked in the Phantom Zone). Green Arrow sums it up in banter in Injustice 2: "you're a lot more grim than MY universe's Batman." "I've lost more friends." "Not funny, got it."
He's arguably far more tested than probably any other Batman, and it's precisely why Joker in the Injustice universe QUIT going after Batman and targeted Superman, because Joker of all people realized he never was going to break Batman the way Superman broke.
Batman has always been shady - in every universe - but this is an incarnation that has reached the epiphany that Dick Grayson's Batman reached: that you NEED to rely on your allies and you can't be a one-man army.
In this universe, he has no secret identity. He has no personal security. He's entirely exposed, and the only thing keeping the Regime from eating him alive is the friendships and allies that believe alongside him that Superman's Regime has gone too far. Even several members of the Regime are only there to try and keep Superman in check - like Catwoman, Flash, and Shazam - only to discover they're incapable of doing so, and when they realize that, they defect. Batman is the leader of a movement, and Batman as a "symbol" is shown in-public as unstoppable and inerrant, while behind the scenes we see ally after ally helping pick him up after each fall and stumble.