One of the most noticeable is Tanya's model. The original model had lighter skin, different face, different hair, and the palette saturation made the model look lifeless. This model is still seen in the story mode of the game. The "pyromancer" variation was originally called "fire goddess" as well:


Sonya's model had manlier face and a beret (instead of the SF hat) at some point:


Here's a screenshot from story mode of a very sloppy Johnny Cage (and Sonya) model. It was heavily tweaked compared to what we ended up with. In this screenshot we can also see that Jax was originally wearing his SF uniform during the farm scene instead of his farmer costume, which makes no sense seeing how Jax wasn't working for the SF at that point:


Cassie Cage's face and neck were heavily tweaked as well. In fact, the "after" screen from the right is still not what she looks like now:


Anything else?