Well, the new storyline should change things around a bit. MK4 back then started with Kitana and Sindel returning things to normal on Edenia, only to have Tanya betray them by letting Quan Chi and Shinnok pass through Edenia.Yeah it seemed like story wise they set up MK 10 to follow the MK4 onward events which would be a terrible idea. Thought the whole point of MK 9 was to go back to the drawing board and bring back in the old fans. It was bad enough they felt the need to include Quan Chi.
With Kitana and Sindel dead (and well, nearly every character) Quan Chi and Shinnok are mostly free to do their own thing (since Shao Kan was also killed). Some characters might return, but with tons of differences Scorpion learns that Quan Chi killed his family during the MK4 story; so..who knows.