Many of these characters have so much potential, I'd like to see a large story involving them.
Kia, Jataaka and Sareena, Shinnok's personal assassins, should return as the new rulers of the Netherrealm. A sexy trio of badass females. Drahmin and Moloch should return as their lackeys. Their actions should lead to Shinnok's return. Quan Chi can return along with Shinnok or he can reform the Deadly Alliance with Shang Tsung.
Nitara is a hot vampiress, she should return and form an alliance with Mileena and Skarlet. Another sexy trio of badass females. Imagine them going against a surprising alliance of Scorpion, Sub-Zero and Noob Saibot.
Reiko, the guy who served both Shinnok and Shao Kahn, should return as the final boss. His MK4/MKG ending with Shao Kahn's mask lowering onto his face was one of the best and one of the most intriguing endings ever. Motaro should return as his servant. Mileena, Skarlet and Nitara joining Reiko would be amazing.
Daegon and Taven should return and form an alliance with Rain, the trio vowing to conquer everything. Mavado and Hsu Hao should return as their lackeys. Tanya should also join this Sons of Argus/Red Dragon faction as Rain's wife. Shujinko as the seventh member of the faction can work. They should have interactions with Kitana, Jade and Kotal Kahn as enemies, but also with Reiko, Mileena, Skarlet and Nitara as... frenemies.
Kobra and Kira should represent the Black Dragon along with Kabal, Kano, Tremor and Jarek. All of them should fight against Rain, Tanya, Daegon, Taven, Mavado and Hsu Hao. Tasia as the seventh member of the faction can work.
Havik should return as one of the bad guys. Hotaru should also return as his main enemy.
Fujin should return as one of the good guys.
Li Mei should return as one of the good girls, I find her attractive. Ashrah should join her in a battle against Kia, Jataaka and Sareena. Chameleon and Khameleon can also join Li Mei.
Onaga and Blaze should fight against each other, it would be an epic battle. Or they can form an alliance. I would have them return as neutral-evil character. They can have interactions with Kronika and Cetrion, but also with Reiko, Rain, Shinnok, Shao Kahn and Sindel.