General Zod has a connection to Krypton and he has a human face, so it makes sense to revisit him for this. I think Brainiac is a bit of an outlandish villain to be honest, and the filmmakers may have thought using Zod for the first go around might have been beneficial so they could potentially set-up a more alien villain like Brainiac.
I have a feeling we'll get Luthor and Brainiac in the sequel (if we get a sequel - but I have a feeling we will) and then probably Metallo or someone along those lines for the third film, however he seems kind of weak for the third entry. It might be better to have Luthor and Metallo in the sequel and then save Brainiac for the third. I'm just thinking aloud, of course.
Either way, they are clearly establishing a mythology, like Marc Webb did with The Amazing Spider-Man
by introducing OsCorp in the first film and then introducing Norman and Harry Osborn in the sequel. Like Admiral_Young
said, we'll probably get mentions of LexCorp in Man of Steel
and then the filmmakers will likely build on that for the sequel(s).