I think we need a white ninja, or a new god, only he's neutral or evil. Shinnok shouldn't be the only evil deity in MK, and we've never had a neutral god. I don't want another good god, we already have Raiden and Fujin for that.
Somebody suggested Ashrah should be revamped as an angel/spirit working its way up to godhood. I'd love to see this happen, as Ashrah's current story isn't going to gain much traction, IMO.
I'd love to see a cybernetic sub-boss (a creation of Sektor after he became Grand Master of the Lin Kuei) comparable to that of Goro, Kintaro and Motaro. Hell, a demonic cyborg sub-boss wouldn't be bad, either. I liked the idea of Noob building an army of cyber demons programmed to serve him, but that story didn't really get far because of Armageddon of course, so I think they should explore a bit more in future installments.