How many special moves do each character have because I know I saw batman having two of them. Or did they just change it
They changed it.
Batman's "original" super involved doing a combo ending with the opponent hanging from their feet by the grappling hook, and Batman dropkicking them.
I know this, because I had the picture of this being done to Flash in my Playstation 3 for a time. Netherrealm recently swapped that "super" for the current shown with folks being run down by the Batmobile.
I remember Netherrealm doing something like this with Mileena and her X-ray attack back when vids were being shown for MK9.