I would have to go with:
1. Shinnok - he should be the final, unplayable, boss, and should be super tough to beat. He should use his amulet during the fight as well, to throw projectiles from, and do other special moves with. He should have two forms, first one should be human and the second should be the monster he turns into in MKM: Sub-Zero once you steal his amulet. You should be able to steal his amulet too, just like in the that game, and that would weaken him. Or perhaps after you steal his amulet he turns into a monster, to pay homage to the awesome game that was MKM: Sub-Zero. I always thought Shinnok was a much more sinister and scary boss (than Shao Khan). He reminds me of Emperor Palpatine in a way.
2. Bo Rai Cho - I loved that character in DA and Deception. I envision him as a wise old martial arts master, who loves his booze. His style should be drunken Kung-Fu. He should be able to take drinks from a mug during the course of the fight, and as he does so more moves would open to him. Just like that character in Virtua Fighter (his name escapes me).
3. Reiko - yet another awesome MK character. As Shao Khan's general, he could inherit some of the latter's moves, plus his helmet, or at least a similar looking one but with some twist, to make it more Reiko's. He should also have ninja-type moves, such as throwing shurikens and smoke bombs.
