Even the worst villains have the best intentions at heart.

No evil conqueror is conquering for the sake of conquest. They do it because they have a vision, something they have reasoning and justification to believe is better than whatever they're conquering.

But conquest is still conquest and that doesn't mean all of his ideals are carried out righteously. Look at the people he employed - his right-hand men were ruthless murderers. He put them in a position of power because he believed they were the best for the job. Guess how they handled it?

Moral ambiguity is something we don't see often in video games. It's here, and I LIKE that it's here. Remember, ultimately Gaius awakened Ultima Weapon and was prepared to crush any opposition in order to reach his goals.