It's very difficult to point to a real antagonist, nor any real villain. That's what works so well for me.
Agito is a victim. It doesn't excuse his crimes, it doesn't make his sociopathic personality healthy and normal, but it doesn't mean he is 'born bad'. He's mentally ill. His recent confrontation seemed to be very poorly executed, and lacking in restraint. He's obsessed with gaining the power he lacked, and losing power seems to drive him into a rage. He's been very calculating in the past, and recently he's gone crazy.
What exactly do we know about Guyot's background? Or that of the Rogues? Or Valcuria? Are they motivated entirely by greed? If so, then perhaps they can be said to be entirely bad.
What about the scientists who knowingly participate in the making of monsters who will kill and subjugate innocents, to save themselves? An argument could be put that they're making an immoral Sophie's Choice.
And the Creators... why were they creating weapons? Were they conquerors, or seeking the means to defend themselves? From their perspectives, eradicating life on Earth would have been no different to a lab technician sterilising a smallpox sample. Or a DEFRA official burning a herd infected with BSE.