Firstly, we now OFFICIALLY know that the next MK game along with the new MK film will introduce a new character. My gut tells me he's going to be the next protagonist of the series from now on (supposing he's going to be accepted by the fans). This character is going to be this "super-market employee that one day realizes he has got magic powers" etc as Kevin Tancharoen unveiled a few months ago. During MK's panel at Comic Con, Boon, Tancharoen and Sloane all three confirmed that.
As for our conversation and imagination goes, the things that I got or I can hold from MK9's story mode is that everyone is dead BUT : Scorpion, Reptile, Ermac, Rain, Mileena, Cage, Sonya, Raiden, Cyrax, Sektor, Kenshi, Skarlet, Kano, Baraka, Quan Chi, Sheeva Goro and Kintaro.
From the others that were "MIA" or even "KIA", I think that we can save Liu Kang (having a Kabal-like burn), Cyber Sub-Zero (Sindel's kick wasn't such a disaster, he can be fixed-he's a robot!), Smoke (I like the scenario that Sektor and the Lin Kuei can collect his body and turn him into a cuborg etc...etc...) and Noob Saibot (Nightwolf kicked him in the "Soulnado" which doesn't necessarily mean that he's dead or anything). So there you have it...
I'd love to see whatever Boon's and Vogel's mind can come up but I'm really - really cautious as to whatever this super-market employee can bring to the table... :/