Mass Sprite Sheet Expansion Battle & NPC

how will the ending look with these swapped characters?

The ending is just normal events with current characters sprite IDs. There is no way to branch on the sprite ID currently, but you could write an event command for that. If you talk about the graphics such as the apple for Shadow, well these are hardcoded in the ending routine and can be removed. I identified a long time ago where they are loaded in bank C3 and you could either; removed the relevant code, display an empty graphic or load a default graphic of your choice for the 14 transitions. The tedious way would be to make 100 graphics for 100 characters and branch on the good graphic offset depending on the actor sprite ID, this for all 14 ending parts. The tedious part here is really making 100 graphics though.

There's also the names to consider but that's another story.