Ermac and Mileena are dead and Reptile is MIA explanation-wise.

But Baraka was summoned. If he is alive in the past so are Ermac and Mileena or am I missing something?

And it has to be after Mileena was created bc otherwise Shao Kahn wouldn’t react the way he did when he was told Mileena was killed.

Story wise, anything can happen. I guess Kronika just didn't have any use for them.

And why aren't they included in the game? Probably other characters had more important roles for the story so they took their spots. It's also a marketing thing. Just look at Shang Tsung. People were so hyped when they saw those ninjas even if they weren't on it's own. But in the next game they probably will be and it's gonna be a big selling point.

Mileena should have been in this game. Her Mortal Kombat X arcade ending reveals that there are many more of her.

Well they couldn’t bring anyone anyway. Maybe Shang Tsung should have got a possibility to morph into Mileena too, and not only Male ninjas.

also why isnt there Kenshi, as another telekinetic character, or Takeda and Kung Jin, when the girls are present. Takeda and Jin at least could have cameo in Story mode, explaining they are doing something else in somewhere else or something like that.