Brainiac is the biggest no brainer in the history of no brainers. His movie version could be a totally unique creation by using all the versions from the comics and more. He could be such a powerful and overwhelmingly scary villain that it's not even funny.
And use Luthor too, but not as a Brainiac accomplice. Have him be the guy that actually BELIEVES in something (nothing's scarier than that), like the Brian Azzarello "humanist to the extreme" version. He should be such an alien hater that he helps in Brainiac's demise, but at the end he appropriates himself of his tech... because if aliens should have a presence on Earth, it should be under human control and on human terms. HIS terms.