I guess if I had one major griping about the storyline in MK 9 is the fact that it took a piss on Armageddon's Konquest mode! I didn't really care for Armageddon that much because I thought the story as a whole was completely stupid. But it still annoys the hell out of me that I spent days playing as Taven trying to complete that story mode only to find out that it was all for nothing. Taven, the character that this game heavily focused on, didn't achieved godlike powers. The one who did achieve godlike powers was the guy who had few lines of dialog in Armageddon, Shao Kahn!
All that work I put into Armageddon was completely invalidated within the first few seconds of MK 9 opening intro! Thanks Ed Boon!