IMO, the dark ones are fine as they are now, needing only maybe some stuff to make them more flavorful. ATM its said they came due to the teleportation accident in the UAC facilities. Would be cool to have a mission to invade a UAC lab itself, with the caveat being that, if you take the mission, you get loads of UAC equipment (like UAC plasmaguns and maybe an intact BFG), but after that the dark ones basically disappear.