Ooh, now that makes it tricky. I wouldn’t say the Administrator is a favourite villain but the Sensorites are a really interesting alien species. Don’t know how I can compare them to the human villains so leaving my answer as is!
Now I’m just sitting here thinking about who the villain is in “The Aztecs”.
It’s actually Barbara isn’t it?
She prances around claiming to be a living god trying to force her own morals on an unwilling foreign culture.
Tlotoxl is actually totally justified in his actions, he’s the antagonist of that story but not really a villain.
My vote for Tegana represents my actual vote, the true villain of Marco Polo; trying not to die of thirst in the middle of the desert. I love how low-stakes yet materially horrifying some of the threats are in Season 1. Honorable mention goes to the secondary antagonist of The Daleks, dying of radiation poisoning.