They Have a Coherent Worldview
Baldur's Gate 3's antagonists operate from positions of genuine philosophical conviction, not cartoonish evil. Ketheric Thorm is broken by grief in ways the player can trace. Their conclusions are wrong, but the reasoning behind them is legible. When an antagonist makes sense, defeating them costs something emotionally.
They Reveal Something About the Protagonist
Micah Bell in RDR2 is terrifying not just because of what he does, but because he represents a version of Arthur that made different choices. Dutch's collapse into paranoia mirrors Arthur's own potential trajectory. The best villains function as dark mirrors.
They Have Something Worth Preserving
The hardest trick in game writing is making the antagonist someone the player mourns rather than is simply relieved to have defeated. Phantom Liberty pulls this off with unusual skill — players spend hours genuinely wanting to help its antagonist before understanding what they actually are.