[Mr_Paper]

I'd like to recommend Ikari Gendo from Neon Genesis Evangelion as
possibly the best villain. He's cruel, ruthless, evil and it's my opinion
that he must be a genius when it comes to strategies and planning.

Cruelity - There is no question about the unheard of levels of cruelty
he is capable of. He is a man who is willing to use and sacrifice children,
even his own, as pawns and weapons in his schemes without any
remorse. He'll knowingly and happily send them off to die or kill them
himself if it would further his goals. Should one die or fall in battle, his
response is matter of fact and emotionless "They are replaceable."

Ruthlessness - Every person, place or thing is only a mere stepping
stone to furthering his ambitions. If they don't wish to comply to his will
he will either force them/it to obey or crush them/it with the power at
his disposal. He manipulates nations, countries and people so they will
play out whatever small part they must to help him then quietly gets rid
of them once they're no longer useful. To him everything and everybody
is a tool to aid his in his ambitions.

Evil - This should be obvious, it is implied numerous times throughout the
series that he either helped make the second impact happen or knew it
would happen and did nothing to prevent it. Not even warn the other
researchers on Antarctica before leaving moments before Adam's arrival.
If he did in fact make the second impact happen, then it only compounds
the darkness of his soul for he engineered the third impact as well. I'm
sure, in the greatest sense of the word, one must be evil if they are
willing to sacrifice the lives of every single human being on the face of the
planet without any feelings of remorse over, guilt for or hatred towards
those six billion people.

Intelligence - To out-smart a council bent on divine intervention,
manipulate nations, corporations and peoples. To plot, plan and engineer
the destruction of the world almost single handedly, there can be no
doubts over his intelligence.

In the series SEELE is actually portrayed as the villain, however, as Ikari
Gendo is the one who makes it all happen (The Chairman even says their
project wouldn't have gotten off the ground if not for him) I peg him as
being the actually villain. Especially since...

Spoiler:

Ikari Gendo betrays SEELE in the end.