(Note: I may be wrong about some things I say, so just bear with me please)
I think their is a difference between a Villain, and a Antagonist
A Antagonist it someone who stands in the way of the hero for some reason, however they are not "Evil" They have motives that they believe in, and most of the time, those motives are good (Or where), they just ended up doing something bad to achieve it,
A villain does however, has no motive, or a motive that is not good,
For example (And I'm going to be taking some examples from other games/ series so bear with me)
William Afton is evil, he killed for the thrill, why, because he/ his family suffered, so others should too, thats evil.
Fecto Elfilis from Kirby and the Forgotten land is another example of a villain; they are evil... just because they can be, they have no motive, unlike most other villains in the kirby games who have a motive/reason; The Dark matter species where born of negative energy, and where made to be evil, magolor wanted power, however that power cost him his soul, Marx...uh Marx... He was hungry because he had no arms to make a sandwich with.
Now for some examples of Antagonist's; I'll be using to examples from the doom series
First is the Khan Mayker: She is invading Earth because her world is dying due to the lack of Argent Energy; is she a good person for this? No, but she means... somewhat well
Theirs also Samuel Haden in Doom 2016: He wants to solve the energy crisis humanity is facing by using Hell's energy, so he betrays the slayer and takes the Crucible for this goal; after this he says a line that sums up what I'm thinking here
"I'm not the villain in this story. I do what I do because there is no choice. Our time is up. I can't kill you - but I won't have you standing in our way. Until we see each other again."
He does what he is doing because he has to, AND he knows he can't kill the slayer, but he can't have him in his way either.
Really, the key to making a villain is to give them no true redeeming quality's, make them pure evil, or make it so their motive is so far gone, that they end up a villain.
I could say more, but I'm going to end it here, for all our sakes.
Thanks for your time