Lex Luthor should be the villain for the sequel. Superman took out the last of his kind, and now he has to face the people of Earth who still fear him and want him gone like the Kryptonians. However, the military (as we saw in MOS) weapons were not effective, thus they have to turn to Lex Luthor to help them build the technology to defeat him. They betray Superman and work with Lex, and then Lex turns on everyone, and now the army has to ask the Man of Steel for help. And since Kal-El is a man of nobility, he helps them regardless and wins their trust...The final installment will have Brainiac, who becomes Superman's most menacing foe. His intellect and physicality proves to be an overwhelming challenge for Superman, and he has to dig deep and find a way to defeat him (like Bane in TDKR).
Darkseid should be saved for Justice League, maybe even teaming up with Doomsday. They both would be more than enough of a challenge for the JL. They could even create Darkseid's planet (Apokolips) like they did Krypton, and have him plan an invasion of Earth with Doomsday.
What do you guys think? Does this seem like the most probable order of villains?