I've only ever watched other people play Injustice 2 (fighting games aren't my thing) and read only some of the comics, but yeah, there are quite a few changes.

In addition to the deaths and alternate earth arrivals, I know that quite a few people swap sides or ultimately decide to stop taking any (like Aquaman).

In just the playable roster for 2 these are the changes from the first game

Aquaman (Regime Defect)

Bane (Regime Defect)

Catwoman (Regime Defect)

Flash (Regime Defect)

Green Lantern (Regime Defect)

Im on batman Side

i do believe some people deserve death

But superman went full dictator

Classic example of give me an inch and I'll take a mile

Batman. How can anyone be on Superman’s side? It’s literal fascism.

Plenty of people are on Superman's side. Just look at the roster.

Oh I thought they meant actual people.

IMO neither are correct, however Red Hood is. In his ending he even says “With the invasion over, Bruce and Superman started fighting again. I wasn't down with either of them. On the one hand, the Regime's right. Scumbag murderers and rapists deserve to die. But on the other hand, I'm no fan of government authority. Especially the dictatorial variety. So while the World's Finest fight each other, I fight for the people. The weak. The innocent. Anyone who can't protect themselves. When they cry out for a savior, I'll answer. As for the criminals who threaten them? They need to know that their actions have consequences. That the Red Hood is coming for them.”

Superman hopefully

Red Hood's ending may hve a point. But, my thing is, we have to uphold the ideals of morality and justice. Going to far, you'd end up just like this Clark or any criminal aside from the clown who would do it all again.