It has been a well known fact that Mortal Kombat as a tournament doesn't follow traditional rules of brackets and elimination (
even that awesome College Humor video recognized that 
). Heck, there's no elimination or actual rules other than "if eveyrone from that realm loses, we have the right for merge with said realm". In the original cannon, the moment Shang Tsung took control of the tournament; he tainted it by not only alllowing warriors from other realms to participate on it (it was supposed to be a tournament between the realm evading merging and the one merging it); but Shang added fatalities into the mix, to avoid possibilities of strong warriors returning later an have an advantage.
The story is not "oscar worthy" but still pretty great in terms on content. The original games had no actual "main story", but they created one during the years from bits and pieces of each endings; instead of having one cohesive story. (For example Jax and Sonya created the OIA after winnign the "tournament", but cannon-wise they never won; but still created the OIA) In this game, this is what they did (or at least tried to), because to me the only "bulshit" part of the story was killing every "good" character in oen scene; when if the intention was to kill them tehy could've spread their deaths a little more.
Also agree what was said earlier. Quan Chi was (and other characters too) introduced in this game earlier basically to imply that he has been through the story all the time and that he has been in the shadows twisting things to his advantage. That was well known through the years, even the original cannon recognizing Quan Chi as the real disruptor of the realms; because he's the one that literally caused everything that lead to Armageddon; yet many ignored about it.
As a note, the reason Raiden didn't intereferd to stop Sub-Zero from been taken away by the Lin Kuei was because they were right in front of Shao Kahn and Raiden is not allowed (well, he assumed at least) that he couldn't directly interfere with Shao Kahn there (as the yall susumed he was just their mentor/guide and not a contestant). It wasn't till later that he realzied that he could, which is why he kills Motaro; but then that causes Shao Kahn to get pissed off and eliminate Shang Tsung which results into Sindel bveen stronger and killing everyone.
Yeah, many things were done in the plot that it was obvious were done for the sake of moving the story rather than actual development, but still no biggie. In the end it's a matter of preferences. Overall impressions has been quite positive of this game's story mode, many really liked how it was done because reminded them to the original movies from the 90s. I liked it, had no problems with the retcons, some were handled good (like Mileena's creation); some were interesting (Cyber Sub-Zero), some were unexpected (Shao Kahn eliminating Shang Tsung and giving his powers to Sindel; thus Sindel stays on the evil side).
And yeah, retcons/retelling may be annoying for some, but are done to just start anew. Heck Marvel did recently with all their main franchsies (X-Men, Spider-Man, etc.). In the case of MK it was needed the story got too big and while it was interesting and big; people in general didn't cared of gave a fuck about stuff like were Quan Chi got his medallion of what the hell happened to Tanya, etc. Yeah some may not like the changes or many technical aspects (but..bu..Jax wasn't around MK One!!! wtf?!!!); but was cool. The story team is working on the next game right now, so hope it's as good as this one was (well, if it's MK related at least).
