Aquaman versus the surface world. If you thought his influence over sea life was lame, his legion of Giant Enemy Crabs would like a word with you.
And then when the Injustice Universe version summons the Kraken.
Aquaman: You think only the surface world has weapons of mass destruction?
Then, if any more proof of Injustice Aquaman's ultimate badassness was required, his ultimatum (given as armies of armored Atlanteans and giant sea creatures invade the world's shores, to Superman's face no less):
Aquaman: I am not some pathetic self-appointed leader of an insignificant country who can be bullied into submission. Every port. Every ship. Everything that flies over the ocean does so with my blessing. Your world would grind to a halt if I willed it. Every land mass borders the sea. Your entire world is inside mine. Consider this a show of strength. Now get the hell out of my ocean.
After that is Superman's response. While it could be considered a Kick the Dog moment for Supes, Aquaman isassaulting countries around the world that had done nothing to Atlantis and because according to him, 70% of the planet belongs to him and the human race exists at his mercy (and going by Flashpoint, this is a TERRIBLE precedent). Doubly so because Superman did it in the same way the normal Superman would have done it by simply relocating his entire kingdom without hurting anybody, except Aquaman's ego.
Also Batman's response to it, namely breaking into the White House and spelling it out for the president that he's Bullying a Dragon.
Batman: The police won't think to look for your body on Saturn!
A minor one, but one person manages to successfully get away with calling out Superman on his slow shift to Knight Templar.
Alfred: Not staying for tea, Master Kent? Superman: I'm afraid not, Alfred. And you don't have to call me "Master". Alfred: Good. Let's remember that.
Insurgency Harley Quinn's Heel-Face Turn is one for her. For a lot of her history, the different versions of her have been portrayed as psychologically and emotionally dependent on the Joker, continuously going back to him no matter how badly he treats her. In this version, when he dies she isn't consumed by vengeance; she actually recognizes what a terrible person he was, and manages to rebuild herself as a force for good... or at least a force that's willing to side with Batman. The payoff is clear throughout the entire story: though she for a time has a relapse and joins up with the alternate Joker, she is clearly broken up about doing it. When he finally shows his true colors, she lets go of her compulsion to him completely and moves on - and given her character, that takes a lot.
As a general rule, every time the heroes callout their Regime versions.
Of all these moments, Wonder Woman's deserves special mention. She calls out Regime Wonder Woman on how her actions have stained Amazon pride and convinces Regime Wonder Woman's Amazons to join her in battle against the Regime.
Wonder Woman: Hold, my sisters! Hold! While I am not of this world, I am Amazon! And I tell you now, this path is folly! We are to unite the world's people! Lessen man's rages! Overcome them! With compassion. And love. (Pointing to Regime Wonder Woman) She has enabled one man to inflict his rage on an entire planet. Let him be consumed by his darkest passions rather than extricate him from despair. Sisters, let us return to the right side of history. Let us enter battle, but as humankind's protector. Not it's destroyer. We are Amazons. We are here to save mankind.
If done correctly, the mini-event where Batman has to fend off a barrage by mind controlled Green Arrow. It starts with dodging the projectiles one at a time, and ends with Batman catching two arrows in his hands and kicking a third one!
Lex Luthor's chapter. You're playing as Superman's usual archenemy, but in this world, he's actually a heroic businessman and secret bankroller of the Insurgency. And in this world, he's The Cape Superman used to be and proceeds to decimate Regime forces and lay the smackdown on the Joker. Here, Lex is the only Badass Normal to come even close to defeating Superman. And here, Lex is inspiring enough to talk Harley Quinn back to the good side and convince some Regime forces to become heroes; most of the Red Shirt Army fighting with the insurgency have emblazoned Lex's sigil on their armor, and these guys are in the thick of a melee between a fascist army and unkillable warriors!
The beginning chapter before the trip to the Regime world. Not just on the Justice League and the Titans together facing up a group of villains altogether and overall winning, these are the moments in the story for you to see the mainstream universe versions that never got brought to the Regime universe: Shazam, Nightwing, Raven and Hawkgirl, doing what they do best: Defending the Earth with all their might (along with the other heroes that eventually get transported).
All of Superman's chapter. The entire game was leading up to his appearance in the alternate universe, and he does the build up justice, starting with him materializing in the Injustice universe starting with the S-Shield and with Crowning Music of Awesome. He steamrolls Black Adam, canonically his perfect counter and one of his biggest weaknesses, Sinestro, Regime!Aquaman, and Doomsday all in a row. Everyone on that list is a candidate for the biggest badass in the DC universe, and Superman just rips through them. And then, before he's even had a chance to recover, he takes on Regime!Superman and beats him down as well.
Special mentions goes to freezing Regime!Aquaman's tsunami and throwing it into the horizon, as well as tackling Doomsday into the sky.
Cyborg vs. Regime!Cyborg, or to be more specific, their mutual attempts to hack the other's systems which ends in a draw. Now this is something you'd expect, what with the only differences between them being their appearance and alignment, but what makes this an awesome moment for Cyborg is that Regime!Cyborg had a very healthy head start. And Cyborg still managed to catch up. Equals? Not even close. It gets better. After the hacking challenge, Cyborg puts up his dukes and says "For real. Like men." Then he beats his counterpart down old school. And later? It's revealed he stole Regime!Cyborg's password during the hacking. Even Insurgency!Deathstroke likes Cyborg after that.
Insurgency!Deathstroke: First rule of warfare. Take out command and control. This satellite's the key to Superman's regime. […] Superman's my priority, not your Batman.
Even better: before he even touched the reactor control panel, he surprised Regime!Flash and Regime!Shazam with a trio of landmines, instantly knocking out the former and dazing the latter enough for Deathstroke to fight his way out. And then, he manages to complete the sabotage just before a recovered Regime!Flash grabs his wrist to stop him!
Aquaman's entire chapter. He first fools Atlantis and Superman's envoys into believing he is their version, only breaking the facade when he reads the appalling conditions of the treaty. He then beats up both envoys, Flash and Shazam (separately in-game, though plot-wise, it was probably simultaneously). When his Regime counterpart arrives, he delivered a What The Hell speech to said counterpart, beats up his royal guards barehanded (only using his trident for defence against two opponents), defeats his counterpart, and is fully prepared to fight even more guards when Ares shows up and paralyzes them. He then makes demands of Ares and beats up him, too! Aquaman admits that he's weakened, though, but it doesn't diminish the feat, especially given all that happened immediately before.
In issue #20 of the comic, Lex Luthor (Injustice universe, the one who's actually a nice guy) proves to the Justice League that he can be trusted by revealing that he knows the secret identities of every member (this is after Superman had revealed he's Clark Kent to the world, but Lex had been trapped beneath the ruins of Metropolis since the blast).
Lex: I'm a very intelligent man. Your secret identities are no secret to me. However, I have protected your identities, and I have protected your loved ones without your knowing. You've had to trust me for a long time. You just didn't know it. Now, I'd like to join you.
Not to mention Robin telling everyone how stupid they were being for playing right into Batman's hands.
Robin: I can almost see the strings.
And the best part? Batman still had him fooled.
Issue 24, a full-scale invasion with thousands dying at the hand of Darkseid's troops. Superman goes straight into the atmosphere, and circles the globe while on fire, killing every last one of them in seconds.
Plus Superman and Flash's conversation just before. There's just something epic about how time seemed to stop around them.
Scorpion's ending. After "The Fool in the Red Cape" had been dealt with, Scorpion is approached by Trigon, who mistakes Scorpion for one of his troops and accuses him of desertion. They battle, and Scorpion wins and takes Trigon's throne. That serves to show that, no matter which continuity he's in, Scorpion's a force to be reckoned with.
In Issue #31 of the comic, Batman convinces the president to send US warships to threaten North Korea as a distraction, so that he and his supporters can raid the Fortress of Solitude. The fact that Bruce just calls the president in the middle of the night and he immediately agrees to do it shows how much authority Batman has, even though he's been unmasked.
Later in the same issue, Catwoman manages to unlock the door to the Fortress of Solitude, seemingly without much effort.
Catwoman: You say "impenetrable fortress" and I just hear "Christmas morning with presents to unwrap".
Issue #36: In what is easily the most epic moment of the comics, we see Superman finally meet his physical match in... Alfred Pennyworth. That's right, Alfred brutally beats the living crap out of Superman, courtesy of the pill Bruce brought back to the cave for analyzing, roaring at him all the while for hurting his (Alfred's) family, leaving Superman a bloody pulp on the ground as Alfred picks up Batman and teleports them both to safety, declaring Superman isn't worth saving. Battle Butler doesn't even come close to describing it.
In the Annual #1 Comic Superman gets Lobo off his back by flying him to the sun and explaining that he won't regenerate if he drops him there.
Harley herself gets points for stealing a super-pill off Lobo, ripping his head off, and then convincing him to drop the bounty on her and go after Darkseid instead.
Guy Gardner: You think we came all the way out here without a plan? Mogo. A living planet with a will-powered weapon. Why do you think we dragged him across space? How much will do you think something that size has?
Regime Aquaman: You are not wanted here!. (After his defeat)
Superman: I may not be wanted, but I'm clearly needed.
Selina: Urgh. Shut. Up. You know what? All the other Robins were good for Batman. But you, Damian—your father is so much better off without you. You're just this joyless, entitled, moody, whining little ***. And you hurt Bruce. I'm going to punish you for that.