Assuming there's a Darkseid in the alternate reality, if Darkseid were to be a playable/boss character in the game, the Superman of the alternate reality could have help from the alterante Darkseid in getting revenge on the mainstream superheroes and supervillains considering they are both alien dictators and the mainstream Superman and Darkseid would have no choice but to team up against them and each one could either have a different fight against them (Mainstream Superman VS Regime Darkseid and Mainstream Darkseid VS Regime Superman) or the two Darkseids could have their own fight and the mainstream Darkseid aids the mainstream Superman against the alterante Superman after defeating the alterante Darkseid.
I'll be disappointed too if Darkseid isn't even DLC in the game. And I actually think the Regime Superman teaming up with the mainstream Darkseid makes more sense, considering the Regime Superman didn't kill the mainstream Darkseid's son and both hate the mainstream Superman. So maybe the mainstream Superman could team up with the Regime Darkseid? I can see Regime Darkseid thinking at first the mainstream Superman is the Regime Superman and fights him and Superman manages to convince him that he's a different Superman from the Regime Superman after defeating him and could team up with him against the Regime Superman and mainstream Darkseid to help him avenge his son.