How closely did Earth: Final Conflict follow Gene Roddenberry's original vision for it? Were the Atavus in Season 5 thought up by Gene Roddenberry or is that something the producers just added themselves for flair?
The original "vision" was bare-bones. The initial idea was that the aliens made critical people on Earth into what were essentially zombies under their control, and they focused on critical people because they could only control a limited number of people, and depended on the mass of humanity being confused about what was happening to allow them to retain control. You can see it here.
As you can see, there wasn't a lot of vision to follow.