In all honesty of all the evil Team leaders in Pokemon, Cyrus takes the cake.

Giovanne was for all respects a Mafia like leader who's goal was for Team Rocket to rule the world.

Maxie of Team Magma's Goal was to expand Hoenn's (and by proxy the world's) landmass to make more habitat's for people.

Archie of Team Aqua's Goal was to expand Hoenn's (and by proxy the world's) Oceans to make more habitat's for Pokemon.

Ghestis, in a similer manner to Giovanni wanted control of the world but he wanted to use N's gifts to do so.

Lysandre wanted to re-enact the events that lead to the sacrfice of 3000 Pokemon.

Lusamine's entire focus was on bringing the Ultra beasts to the real world.

Yet, amongst all of that Cyrus's ultimate goal was to rewrite the universe in his image. He was the only character that was absolutley fine with taking life as he knew it, wipe it clean, and start all over again.

For me, Cyrus is the one who deserves op spot of being the most evil of the Pokemon Antagonists.