After a lot of thought, I've figured out the grand scheme of my main "villains" in the series. Since the story will probably span three stories, these characters will make it into the limelight and then step back for the next one to take their place.
Tier 1: The Orvilles
The main antagonists of the original draft of the story, but with the story expanding their roles will change later on. So while they might be antagonists for the first book, they will also be the protagonist's link to her past and surrogate father figures in the future. In fact, it will turn out that their villainy is a misconception that comes from lies and secrets they must keep. With them appearances are definitely not what they seem.
Tier 2: "Magnus Edison"
Technically a new character, but I believe him to be an essential one. He steps into the role that the Orvilles once had of mentor and leader of a company/organization. He is responsible for a lot of the issues, but not the main cause. He is generally good intentioned and despite his best attempts they have backfired. He has become what he is out of desperation and a desire to preserve what he wants most in life: control.
Tier 3: "Cromwell"
As far as the overall story and world goes, she's the main antagonist, the top villain, the lady to beat. It is because of her actions and choices that everyone is in this mess. And so she will affect and alter the lives of everyone involved, even if she does not directly interact with them. This is similar to the original story, but the history, character traits (he is now a she) and role overall have changed drastically.
I have figured out a great deal about this intriguing lady and plan to make a much longer post later. But here are the key facts:
a. She is a woman with a plan and will see that plan to the bitter end.
b. She is the living representation of Minotaur, a person who has unleashed a lot of death and suffering--whether she intended it that way or not. And she is something both Magnus (based on Minos) and Vincent (based on Daedalus) feel responsible for and wish to deal with.
c. While she has dealt with similar issues to my protagonist, she has made the wrong choices and not learned from them--because of that, her end is inevitable.
d. She believes that her actions are in the best interest of her people.
So far...a good start.
Next time, a bit more about "Cromwell".