I still don't understand why people don't like MK1 but I never play competitively. I don't like these guest characters tho. Who da fuk asked for these lame superheroes?
I think one of the theories being thrown around is that the MK casuals(the majority of audience) don't like fighting games with teams(ie. dbfz, Marvel). Also the competitive audience and players aren't thrilled with it as well. I think a lot of it has to do with how WB/NRS has handled dlc. But that's more of the marching orders from WB, I think. Also the online seems like it's had more than a few rough patches.
As far as the superheroes go I think given the ones that are in there they thought MK as the ultra violent franchise was the better fit. I think having Omniman and Homelander in Injustice 3 would've been far more interesting. Especially if they were in the story mode a la Akuma in Tekken 7. Given that Suicide Squad exists it seems WB is okay with treating Superman and co. like garbage so them getting beat up by Omniman or Homelander shouldn't be that much of a issue.