Blame terrible writers, directors, and animators for all of that. Also, every MK animated series was aimed at kids. MK could easily be turned into a gritty badass animation series with PLENTY of storytelling depth, the problem is who's going to fund it and who's going to watch it/buy it?
Alright. What I mean is, the creation of media involving another's copyright property comes with an enormous amount of issues, negotiation and re-re-re-re-reading of a storyboard usually written by somebody not at all entitled and generally disinterested in the whole ordeal just wanting their money already. So the guy writes something, sends it in, the producer negotiates with the original owner, over and over several times.
Typically in the case of fighting games (and games in general) the owners do not care to see a storyline with more depth than their original game lest the game "loses prestige" or somesuch. A matter of pride in many cases, too.
I'd love to see a Mortal Kombat written by somebody like Bendis or Gaiman. Not happening.