This sounds like a great topic that I will follow closely.
My project is an RPG that features 5 main groups, all of which at points are antagonists or "evil" at various parts of the story.
My first big writing decision was to really try to make sure their motivation was clear. What do they really want? What is driving them to be "evil" or antagonistic? It has to be rational and believable unless they are just completely insane or chaotic (for me at least).
Then I tried to make sure that motivation was tied to the world they lived in, so they really feel like part of the world instead of dropped into it as an afterthought.