For me it's Reptile. Although he was the weakest character in Mortal Kombat 2, From Mortal Kombat 3 to Mortal Kombat Deadly Alliance, he was awesome. He always had a cool fatality and look. But when I was playing through Deadly Alliance again last week, doing Konquest, I'd forgotten how annoying his character is.
Reptile is basically the Mortal Kombat equivalent of Beebop or Rocksteady from Ninja Turtles. He's a subserviant follower, who can't stand on his own. His loyalty to Kahn is so ridiculous that it almost suggest some sort of sexual crush.
So which characters do you love in the game, but hate for their story?