For most people I think it's that they'd rather the developers had spent their time and effort modeling a real MK character that didn't make it into the game, instead. Like Kratos has stolen a spot that could've gone to Rain or Kenshi or who knows.
And MKvsDC's big problem was you can't really make a Batman/Superman game with an M rating so all the finishing moves were weak.

I have a problem with it because MK is MK. And Goddammit, if I want to play MK, I don't want to see someone from some other form of media in it! MKvDC was okay because the whole point of the game was a non-canonical mash up of the two worlds. I was fine with that. But when MK is coming back at its biggest and baddest, what do we do? Yeah, we throw Daegon in a skirt and call him Kratos.

And it's just really random and that's what gets at me most. We didn't ask for this, so for them to throw some random character from some totally unrelated franchise is beyond me. I can ignore him all I want, but because he's in a canon game, he'll feel canon to me. And I hate that because I'll have to spend time pretending he isn't there.

FYI, I'm not mad, I just have strong opinions on this subject.

Beat me to it lol but yeah pretty much everything NS922 said. NRS can't be like "this is a game for the fans, its a reboot/retelling of MK 1 - UMK 3, we're going back to what made MK great" and then turn around and be like "Kratos is in!" If they wanna put Kratos in an MK game then fine, but it better be called MK vs God of War or MK vs Sony or somethin like that, not in a game that continues on the canon story of the MK universe