Seriously speaking, the Covenant.
But I mean.. as far as like a single villain goes, you can't get a better story than Handsome Jacks.
English
-
The Covenant are brutal, conquerors, warlords. Handsome Jack is... Insane, brilliant, misunderstood, and has one of the most amazing backstories I've ever heard. As far as military power goes, Covenant all the way. But do they really make an interesting game? No. That's where Handsome Jack and Hyperion come in.