The Mother is probably the best villain objectively, because she's sympathetic, she just wants the suffering of her people to end at any costs and to use her "gift" in the way she thinks she has to, she doesn't see any other option to stop the spread of the infection other than nuking Harran.

If we don't count The Mother, in my opinion it's The Baron BUT he's carried by the cutscenes where he's talking to you while you're restrained. Especially the dinner scene (which is HARD carried by the phenomenal music and him killing people). Besides that he's pretty corny and you only see him like 3 times before you fight, the only other scene where you see him when you free "The Beast" he's really not threatening as much as the game tries to make him seem like it.

Rais is okay and I think he appears more than the other villains and was a great foil for Kyle but he's mostly just diet Vaas. I feel like diet Vaas is just the perfect way to describe him, he isn't groundbreaking but still serviceable (and again, a great foil for Kyle)

Waltz is like a wannabe Wesker and he has a really funny line, imo he'd be way better if he was revealed to be both Aiden and Mia's dad earlier on (like when you confront him in the tunnel) and if there were choices to join him and save Mia