Since they're apparently going ahead with an MK sequel, they're probably going to have to work off the mess Annihilation made.(unless they completely ignore MK:A, which IMO would be wise)
Since MK:A butchered many characters and stories, what are ways the next MK could "fix" them to make it truer to the game?

Here are a few I thought of:

Scorpion
What's wrong with him: Works for Shang Tsung/Shao Kahn; has weird creatures living in his hand.
What to fix: Scorpion's damage isn't that bad. They could reveal that Scorpion was only working for Tsung and Kahn to get to Sub-Zero.
They just have to take the time to explain Scorpion's origin. Unless the flat out ignore them, I think we're stuck the hand monsters though.

Sub-Zero/Noob Saibot
What's wrong with him: As Sub-Zero he worked for Shang Tsung and as Noob Saibot he came out of Ermac's chest.
What to fix: Like Scorpion it's not so bad. In MK1(game) Sub-Zero was trying to assassinate Shang Tsung, so they could say he was only working for Tsung to get close to him.
The damage to Noob can be ignored, since they didn't make it clear it was Noob Saibot who leaped out of Ermac's chest. They could have the real Noob show up and the guy who came out of Ermac was just some dude.

Ermac
What's wrong with him: He's a brown-noser and he's dead.
What to fix: They'd have to resurrect him somehow. Then they could have him trying to turn good, like in the games.
Other than that, they just need to portray him correctly, because in the movie they made him too human.

Kitana
What's wrong with her: Was never evil and always knew Shao Kahn wasn't her father.
What to fix: This could actually be used for a good plot development. They could make it Kitana's been lying about her past the whole time so the good guys would trust her. Then have Mileena or someone else tell Liu Kang and the others about Kitana's past, trying to turn them against her.

Jade
What's wrong with her: Let's see....she's evil, Chinese, and dead.
What to fix: uhhhhhh......this is tough. Reveal that wasn't really Jade..? *shrugs*

That's all I can think of for now.
Any other ideas?