They have nuance, yes. But that doesn't necessarily mean they're "good" or morally correct in their justification.
An antagonist can have a reason to be an asshole and still be an asshole.
Rare is an antagonist that has 0 reason for doing what they do.
Good Antagonists are the ones that think they're the good guys.
You're reaching. Shao in previous games and Shao now is a totally different character who fills a totally different narrative purpose. The same with the rest of the classic "i will literally eat you" become "i'm fighting for my people" villain list.
At the end of the day there's something to be said for M Bison or Shao Khan being stupid levels of Evil. Nuanced plots aren't well suited to fighting games (at least as they tell them now). I'd actually argue that the scorp/sub plot spanning MK to MK4 is actually a GOOD way to do the nuance (frankly better than it deserved to be given how they handled things back then), but if you make EVERYONE like that it gets old fast if you can't seriously dedicate time to their motivations.
GoT does a great job at this because it's a fucking book series that's willing to do major arcs for all sorts of characters with all sorts of motivations pulling at everyone. Mortal Kombat is a series first and foremost about literally punching your opponent in the dick and ripping their head off.
Watching shao/goro/whoever show up in a cinematic and wreck the thunder god along with several other fighters sets enough stakes for the time they have, and makes it feel like a big deal when you kick his head in. Having literally everyone be given some justification for fighting just gets boring becuase there's fuck all way to build the depth or the stakes to make anyone care.
What's more annoying is that they KNOW this, and that's literally why we also got "evil" universes, which while mostly eye rollingly stupid does bring up some interesting interactions (liu shang vs titan shang), but again, this is for a very breif part of the plot, and worse, doesn't make it to the pre fight dialogue.
I can't stress that last part enough, because MK is miles ahead of the competition there, and almost all the fun has been stripped from that this series becuase they have to stick to the liu verse version of everyone.
Finally, yes Bi Han is the ONLY legit bad guy in the base roster, and it's fucking weird. Yes it seems Quan and Shang are destined to be evil, and they don't really go into the more interesting arc of "you mean to tell me fucking GOD put me in the mines?" (which is like, the one "justification" that this narrative actually brings that might be interesting to explore). Bi Han is just an asshole, but a pretty boring/low stakes one. It seems that might change a bit when he gets murdered into Noob, but some of the best parts of MK1 are the arcs involving him becuase he's simple enough that it works.
Having Havok, Nitara, Baraka, and arguably Reptile all trotting out the same "for my people!" arguments when they don't even have time to show us anyone but the "tarkat" victims is weak writing. Doubly so because once again the rather interesting arc here is MK is now a game where you can literally beat the shit out of god for letting bad things happen to good people, and they don't use that in the slightest.