Injustice 2 Explained: What Does The Ending Really Mean?

This is the ever-present problem in regards to Batman's actions: He condemns killing, opting instead for rehabilitation of criminals by putting them into the Arkham Asylum. However, this ignites the endless cycle (escape, kill/hurt people, get caught again) that almost all of Batman's enemies experience.

Since the system doesn't work, why does Batman keep trusting it?

Well, this time Superman intends to kill all of the inmates. Unlike Batman, he prefers eliminating the effect of the crime, not the cause. These world-views obviously have to clash.

While Batman believes that the criminal has the right to redeem himself, for Superman he needs to be eliminated, as he is fragile and unpredictable. Or rather, actually predictable, as sooner or later he will be back on path of crime.

In Crime and Punishment, Michel Foucault described how punishment changed through the ages, as it moved from a spectacle which culminated in public execution, to incarceration, understood also as separation of the criminal from the public.

This is the punishment preferred by Batman, who wants the criminals to eventually pay their debts to society. He believes that everyone deserves a second chance, as we all can be good in the right circumstances (like Harley Quinn). Superman on the other hand believes in complete elimination, not separation.

Whether done publicly or privately, it's all the same to him.