Still haven't seen "Man of Steel," but if DC was following the Marvel model then Luthor is a character that should've been set up as the Big Bad for either a third Superman movie or a Justice League movie. He should've been introduced as a background character in the first one, either through strategic placement of LexCorp products and staff, or via news reports that show him as a strong and powerful figure. The next movie, he challenges the concept of Superman -- why do we need him, when LexCorp can protect you? -- and then in the third he's the Big Bad challenging Superman directly (or indirectly, by wielding influence or through another villain created by LexCorp like Brainiac or a reimagined Bizarro).
Not sure if elements of that are still part of the plan, but Luthor is a villain that needs to simmer. He's a schemer that would be better portrayed as the one behind a multitude of threats, not the immediate threat itself.