Someone who appears to be the games main antagonist from the start but secretly has long term plans that end up making them a strong supporting character by the end.

As far as true villains go, final boss style, I'd like them to have depth beyond "I will consume all for the sake of consumption". They need to justify their actions, whether self serving or otherwise. If I look at the world from their position I want to see where they're coming from and see why someone would choose that path.