In my opinion, we should still steer well clear of Lex Luthor. I still have a bad taste in my mouth from Kevin Spacey's portrayal of the character in Superman Returns. If Brainiac comes after the Earth in the sequel, that could ramp up anti-alien sentiments from all the damage these guys are doing. That would open the door for Lex Luthor to take the stage as a figurehead for human rights in the face of alien threats. He could lead a movement to take down Superman, claiming all this started with him arriving on Earth. It would be even more poetic if the people he's saved come to his rescue.
You could even tie this idea into a Justice League movie, let's say Darkseid (or Apocalypse in general) comes calling in that movie. Superman's first reaction to another extra-terrestrial threat could be, "(sigh) Why do I get the feeling I'm going to be blamed for this?"