If this is intended to be the first film in a new trilogy then I wouldn't be surprised if Brainiac is shown in a flash back or used as a set up for a future film. Much like Ursa, Zod, and Non were in "Superman: The Movie" we didn't actually see them until the second movie. Doomsday I think wouldn't work unless they were using him in a "Death of Superman" film and they already attempted one several times and failed.