In my opinion, there is one villain whose goals are slightly different than what you'd expect:
The Overlord of Darkness is the creator who gave all beings in the world life. His goal was to get back the seed of Agito because he feared that someday humanity would evolve beyond his control. What's interesting is that he wasn't innately evil at first; he only chose to eliminate a certain group of people with the seed of Agito, not all of humanity. Every time he kills someone, he feels pain and sadness because humanity is basically his own children,
per his quote. He also places a taboo on the Lords to prevent them from killing normal humans, and when a Lord breaks the rule, he makes her commit suicide.
Near the end of the story, after getting sucker punched by Shouichi, he was shocked that humanity had grown strong enough to oppose him. He decided that humanity was no longer worthy of existence, and so he began a genocide and started anew. His plan was ultimately thwarted by the heroes; in the end, there was
a small conversation between the Overlord and Tetsuya Sawaki, the latter of whom convinced him that while he created humanity, he did not truly understand them, and humanity's endless potential for evolution is what makes them special. The Overlord eventually takes Sawaki's word and chooses to observe whether humanity is worthy of existence or not.
Simply put, his goal stems from his own love of humanity, a love that is akin to the owner's love for a pet over which the Overlord wanted to seize control. In the end, however, he put his faith in humanity's strength and chose to observe them instead of taking control of them.