My biggest complaint is in regards to the myriad of plot holes, and quite sloppy ones at that. MK team, DO YOUR HOMEWORK! The things you screwed up are downright embarrassing. I know that most people who play Mortal Kombat don't give a flying kick about the story, (understandable, as you play a fighting game to kick the piss out of someone) but to some of us who actually do care, it's just aweful. MKM: Sub-Zero, while it may have been a complete flop, had no continuity glitches at all. (EDIT: I take that back. It did have two continuity glitches: the deaths of Fugin and Quan Chi.) Special Forces on the other hand...well, that game offers absolutely nothing to the MK chronology, so it's okay. Shaolin Monks, on the other hand, completely messes up the MK continuity. It even reached a point where I was questioning the canonicy of this game. But you see, unlike the other two I just mentioned, this is a great game gameplay-wise. Hence, these plot holes matter quite a bit.
Here is a list of all of the plot holes I was able to find:
1. The deaths of characters who appear in later games, namely Jade, Reptile, Baraka, Ermac, Kano, Goro, Shang Tsung and Shao Kahn. Granted, you could simply write these things off as you do with all of the other games: the fatalities you perform on NPCs are not canon. But there is a problem with this in regard to Jade, Kano, Tsung and Kahn, because after performing the fatalities, their deaths are recognised by other characters. Hence, they appear to have really happened, which is wrong. And let's not forget the one character who should have died, but did not: Milleena. (More on her later.)
2. The costumes and appearances of certain characters--namely Liu Kang, Scorpion, Sub-Zero, Raiden, and especially Reptile--which were not how they looked in MK1 or MK2. Liu Kang had short hair back then, Scorpion and Sub-Zero wore much simpler--and much more ninja-esque--costumes, (the ninja feel to those characters is almost gone now) Raiden wore his white outfit but without that blue...thing in MK1, (he had it in MK2, but it was shorted and of a completely different design) and Reptile was supposed to have appeared to have looked human back then. (In fact, his devolution was supposed to have been one of the major things about his character.) Another character who's appearance is problematic is Quan Chi, who appears briefly at the end. Now, he was supposed to have worn his MKM/MK4 outfit back then, and was not supposed to have those tattoos or that forehead jewel yet.
3. The introduction of the idea that the souls of Outworld's citizens are trapped inside the soul tombs upon death, rather than going to Heaven or the Netherrealm. This presents a problem, as Milleena--who was supposed to have been killed in MK2--went to the Netherrealm and made a deal with Shinnok who resurrected her in MK3. Assuming she died in Outworld offscreen, how would this have been possible?
4. Shang Tsung was supposed to have had his youth restored by Shao Kahn himself. (Although the way it was restored in Shaolin Monks was deffinately cooler.)
5. Reptile has red blood. His blood is supposed to be green.
The way it is set up now, one of three possible conclusions can be drawn:
1. Shaolin Monks is not canon.
2. Shaolin Monks is canon, thus appocryphizing MK3, MK4, MKDA and MKD.
3. Only certain parts of Shaolin Monks are canon, while others are not.
I think this problem needs to be addressed to the public by Midway so that we can know exactly what's going on.