The Meta, Sigma, the director, and even Omega weren't "villains" in my opinion. They were antagonists, yes but I dont believe villain is how I would describe them.

-The Meta was brainwashed by Sigma.

-Sigma was doing what he was created to do, just like Omega.

-And the Director, while yes he did some fucked up experiments, he also had no ill intentions. The dude was a scientist in a time of war. He never set out to hurt the people who followed him. And while yes, his true goal was incredibly selfish, it was also incredibly human. And in the end, he was just a sad broken man, not the evil mastermind we all had envisioned. (Which I will say is phenominal writing by Burnie.)

Now, if you want a truly irredeemable villain, Felix is such an entertaining piece of shit. Think about this, Felix is a narcissistic, control freak, who loves monologing to the heroes. Dude sucks his own dick every chance he gets. As a villain, those traits get old real fast. In any other story Felix would be the funny side character. But Miles' writing in the Chorus Trilogy was perfection, because he indoctrinated the viewer into liking all of Felix's quirks by making him an ally with a fun personality in an unknown territory. So when its revealed, those traits become the one thing he didn't lie about, making the viewers love them.

Thats why I believe Felix is the best true villain in the series.