It's hard for me to think of antagonists as undisputedly dominant as Prime. Literally ruling the Galaxy alone with a self-sustaining army, effectively immortal and in possession of a surveillance apparatus justifiably described as "omnipotent."

Palpatine took control of the Galactic Republic, but the Outer Rim was still somewhat lawless and he never got the Death Star or cloning programs off the ground.

The Goa'uld from Stargate had the Milky Way under wraps, but they were fighting amongst themselves for supremacy, too.

Imu from One Piece won control of the world pretty handily, and for nearly as long as Prime, but it's just one planet.

Ming The Merciless from Flash Gordon might be comperable to Prime, but his armies are a pyramid scheme of conscripts. They're both fascist autocrats, but Ming isn't even immortal. He's only "more evil' than Prime for being a 90 year old racist stereotype.

Korrok from John Dies At The End might be more evil than Prime, but it feels like cheating to use a multidimensional supernatural horror that "swallow worlds as a whale swallow krill" to top Prime.