Most of the characters that were killed in MK9 all died in the earlier timeline after MK3 (see Liu Kang). I'm expecting MKX to have all of the characters who weren't killed on-screen in MK9's Story Mode (see Rain), more characters from the games after MK3 (see Tanya), and some new characters.
I'm sure that MK9 having so many of the characters in it killed off was Boon and Co.'s way of telling the fanbase that yes, there will be cuts to the roster, better be ready to find out that (insert MK9 character here) isn't playable (or isn't part of the Konquest Mode). I'm also sure that Boon and Co. plan for characters from games after MK3 and new characters to have more focus in MKX instead of focusing on the characters from the original trilogy.
I wouldn't be surprised if Liu Kang was treated how he was to make parts of the fanbase more open to Shujinko and/or Taven showing up in MK games after MK9.