Excellent rundown of what happened in this storyline, man. I stopped reading after I realized how much money I'd be spending if I continued buying them digitally every week. I didn't realize it was going to be an ongoing series.
Having said that, regardless of what happens in these comics, NRS will explain away (or not explain at all) anything that occurred if it means selling more copies of the game. If anyone believes for a second that Joker will not be in Injustice 2, they're crazy. I don't care that Superman punched a hole in him, he's faaaaar too popular not to make the roster. I'd say Dick Grayson is nearly on that level, as well.
Also, I really want Damian Wayne in this game. I'd love to see what he could do. There's so much potential for this roster. Can't wait to see what the final roster is.