Possibly the best part of the original game, Netherrealm chose to not only create a universe, but create a second one as well, and make a story that is actually better than most story based games. This is really nice for people like me who cannot find people to play with regularly and find online to be not as fun as local play.
For a sequel I feel the game should stick with the universes it already established, maybe it could expand to a third universe even, which could then explore how the one universe has everything go well for it while the others take dark turns. As for a plot itself I have a few ideas; the first would be the aftermath of Superman's defeat, with the greatest protector of the planet gone a villain such as Darkseid would be free to move in and conquer with relative ease forcing the heroes and villains to come together to defeat him. Another possibility could be another event happens that branches the "good" universe again, and the Insurgency Batman learns that all divergent universes stem from the same universe, and exploring why this is.
The weakest part of Injustice, at least in my opinion was the stage selection. There was only a small number places to fight at, and some of the stages were identical with very minor cosmetic differences. What I want to see is a wider array of stages, the DC universe is full of iconic locations, so why are we limited to so few stages? I want to see places like Oa, New Genesis, the Flash Museum, or even the Legion of Doom's hideout. I just want more to keep me interested longer.
Injustice had a wide variety of character to play as, but there were some aspects that could have been better. First and foremost I feel there were a few too many Batman characters, especially considering the game revolved around Superman. Sure some of them were important to the plot, but Bane and Grundy simply acted as muscle and could have easily been different characters. Then there is Batgirl, who was fun to play as but ultimately added nothing to the story. I also was a little disappointed with the large amount of DLC. Don't get me wrong I'm okay with some DLC, but Injustice had a large amount, too much for the casual player to pay for.
What I would like to see is more unlockables in place of some of the DLC, this could add some replayability to the game as well. As for specifics, perhaps the game could add a new type of character besides the gadget/power dynamic they have now...say magic, adding a new level of strategy for players. I also would like to see an expansion on the alternate costumes doubling as characters, for example more Green Lanterns like Kyle Raynor and Kilowag, or Jason Todd as a Deathstroke skin. I thought his was a clever way to increase the roster, so why not do more with it. Some characters I'd like to see would be a mimic character, someone who can randomize his play style for those who like that, a character like Amazo, Black Alice (for magic characters only), or Parasite...In fact the more I think about it, the more I want Black Alice. I also want a character I've grown attached too in recent years, Animal Man, his personal move could be to change up his moveset between speed, strength, and defensive types. Also as I mentioned in my plot idea, I want a big bad, a REALLY big bad specifically I want Brainiac, a character who can bring an Age of Ultron like story to the game.
The main thing I'm asking for from a sequel is to not simply release the same exact thing again and call it good like some other games out there, or worse yet decline in quality to coast on the title's reputation. But I think Netherrealm understands this, just looking at Mortal Kombat's history they seem to understand how it works, they even rebooted the franchise after making a game that simply did too much. So I am excited to see what they have in store, and hope we get to see it in the near future.