When did you first notice that Liu Kang was no longer the main character of the story and why do you think it changed?

I say that it was Mortal Kombat 4 that the change was made or, at least, started the moment that Raiden gave that monologue about the previous war with Shinnok and the change was completed in Mortal Kombat: Deadly Alliance.

I think the change was made because Shao Kahn's defeat meant that Mortal Kombat was no longer needed as a tool of defense against invasion meaning the story was now less focused on the mortals. The fact that they were dealing with gods and higher level beings and we were now seeing the main characters regularly traverse through other realms meant the story was becoming much grander in terms of scale so it may have been seen as the logical choice to move Raiden into the lead role which he briefly shared with Shujinko in Deception since he's no longer a mentor to the mortals, he now has to lead them in dealing with the other realms.