It is possible that Nolan, Goyer, etc. are saving Brainiac and other villains for future installments. Maybe we'll see Brainiac introduced in this film but not take a full-on role as villain until the sequel. Who knows. We have so little information at this point and General Zod hasn't even been officially confirmed- just mentioned offhand in an article.
I think if we have Luthor and Zod in the first movie, Metallo or some such in the sequel, and then Brainiac in the third film- he is, after all, Superman's big bad and I think saving him is a good idea. Perhaps Nolan and Goyer are planning on using him for the second film, like how they used The Joker for The Dark Knight
- who knows at this point.