Originally Posted by RachelDawes
It's really tough to get three villains to work, plus it reduces one's villain options when the third movie is made.
As the last poster said Superman has a great rogues gallery.
I think the sequel could be Lex and Brainiac and Metallo. Lex is the behind the scenes villain and is setup for a bigger clash with Supes in MoS3. However, he "attacks" Supes through the media and through anti-alien politics.
Lex discovers Brainianc after doing some research and recovering of kryptonian wreckage left over from the battle between Superman, Zod & Faora.
Lex learns from Brainiac the destruction of Krypton and how to kill Superman....kryptonite. However, in exchange for promising to make Lex the most powerful person in the world through technology, knowledge, and power Lex must build a construct/body for Brainiac to be powerful again. Thus, he builds Metallo.
Metallo is combination of cybernetic parts and a human/soldier in peak performance that was killed during either a foreign war or battle in metropolis. Lex has a secret agenda to use cybernetics to show the world that people can achieve super soldier like abilities and possibly cheat death and not depend on superman to save them.
Metallo fights superman powered by a kryptonite. Superman is not aware of the kryptonite's effects on him, but is made aware that something on Zod's ship caused him similar effects of weakness & pain. Metallo almost defeats Superman in their fight, but Supes wins.
In MoS3 Lex becomes a greater threat having a built a suit of power learning from his mistake in creating Metallo. He takes things into his own hands. However Brainiac controls the suit and kills Lex and takes over his body, or the become one.
Or in Mos3 Lex leads a cloning cadmus project and creates Doomsday, by using some of Superman's dan from which he recovered from the battle in MoS1. Or Lex discovers Doomsday was a planned weapon of mass destruction created by Zod and his army or Kryptonian military to against other alien planets or on their own planet against enemies because kryptonians did not have superpowers on their home world.