The way I look at it, and I'm sure NRS will be doing something completely different, but the way it looks to me that things will turn out with the way MK9 ended is as such:
MK10 will happen somewhere between a few months to two years after MK9.
Outworld
With Shao Kahn dead the leadership of Outworld has gone up for grabs. Before his death Kahn CLEARLY declared Mileena his heir, but many are not happy with this. She's not exactly the most intelligent of the people in line for the throne, and many believe she will bring Outworld crashing down if left to lead.
In response to these feelings, Reiko, one of Kahn's greatest and most loyal generals, previously thought to have died during the Earthrealm invasion, has stepped forward and layed claim to Outworld leadership.
The most savage of Kahn's subjects, such as the Tarkatan, support Mileena. As do the centaurs, as Reiko has shown favor to the Shokan. Ermac has stayed with her as she IS Kahn's true heir (or maybe for other reasons...).
The more civilized Outworld races have rallied behind Reiko, including the former Edenians. In addition, much of the leadership of Khan's army have gone with him.
Civil war has broken out and it's a stalemate. As, while Milleena and her forces have access to most of Kahn's resources, Reiko and his forces have access to most of his actual power (military leadership and the like).
Rain acts as Reiko's top general, Tanya as his political advisor.
When war with the Netherealm breaks out, both sides are overwhelmed due to the ongoing war with each other.
Earthrealm
Fujin is not too happy with the way things turned out by the end of MK9, especially with Raiden's actions in the Netherealm, so those two are on the outs. Johnny and Sonya are still on good terms with Raiden, since they don't know what happened in NR and what happened with Liu Kang was an accident, and his own fault since he was getting in Raiden's way when he was trying to save the world.
When the Netherealm begins its attacks Fujin starts putting together his own team. If Liu Kang is alive he joins with him, and Master Bo Rai Cho does as well. They seek out more forces coming across Kenshi and Jarek. If he did not survive it is Kai that joins Fujin, while Bo Rai CHo, not knowing the details of the events of MK9 sides with Raiden.
Netherealm
The only really unified side, ostensibly lead by Shinnok, but it's really Quan Chi that holds all of the cards. He's the one with direct control over most of their best forces, it is only Shinnok's power that keeps him in charge (but we all know that he really doesn't have any)
