It was never meant clear WHY Shinnok needed Shao Kahn defeated/ removed from the equation to attack. Would Shao Kahn have allied with Raiden against Shinnok? THAT I would have wanted to see.
He also takes his time in the new timeline. He doesn't attack for 2 years after Shao Kahn's death. Why? What did he need? Some incantations or sacrifices to complete? It was never explained.
It might be like in Warcraft where Sargeras needed a stable portal to pass through with all his immense power into Azeroth.