Actually, Sindel's an interesting possibility... Given that she appeared in Quan Chi's lineup of marionettes, it looks as though the power of Nightwolf's shaft (lol) of light was that it merely killed them both. That would be consistent with the deal between Quan Chi and Shao Khan for the souls of the fallen.
Something tells me that these souls aren't lost forever. Quan Chi might use them somehow in the story of MKX, but it shouldn't be forgotten that Sindel was much more than a single soul when she died. She was an amalgam of herself and a powerful sorcerer, plus all the souls he had absorbed over the centuries. I don't imagine that even Quan Chi's necromancy can fully control such a being.
It would be a fun and surprising twist if she were able to break free of his control at a crucial point in the story. I'll admit it, part of why I like this idea is that this franchise has never had a female as its main antagonist. Granted, Sindel's rampage was a huge plot point in MK9, but fighting against her as Nightwolf felt really anticlimactic for me, because she was waaay too easy. After seeing all those beloved characters murdered, I was expecting much more of a challenge.
Plus I just don't see Mileena as an auspicious enough villain to ever be a true 'big bad.' The only other interesting possibility for a female big bad would be this mysterious inter-dimensional body-snatcher who appears in Jade's ending. I don't imagine NRS would introduce that concept and have it come to nothing, but then... the same can't really be said of Sonya's ghost-dad. That needs to go away.