Ditto's there like in every game because Ditto makes breeding so much easier.
Somehow the move Transform was programmed, so that's already a step in the right direction. Perhaps the change in sprite would have something to do with how the move's already programmed.
I haven't tried this move animator yet, but maybe you can try making Ditto disappear, and then make the opponent's Pokemon appear where Ditto was? Just a suggestion, and may not be possible...