Harley Quinn, Killer Croc, Reptile, and Quan Chi were originally going to be both playable and later DLC. They were left out due to both the deadline and the collapse of Midway Games.
The idea for this game (when it was still the tentative Mortal Kombat 8) was originally to follow the events of Armageddon, with most of the cast dying in the Battle of Armageddon in order to make way for a new cast. Scorpion and Sub-Zero would be survivors of the event. When it instead became a crossover with DC, these plot elements were modified and reworked into MK9, only that instead of the ninjas, it ended up becoming Raiden and Shao Kahn.