I have little doubt that the movie will tell the origin story, though doubtless in a very different way from the first Superman film, probably with more emphasis on Krypton before the fall.
Assuming that the audience already knows and cares about the character is a fatal mistake that I'm confident will not be made again with Superman. That is one mistake among many that was made with Superman Returns and also with The Incredible Hulk, I might add, though that was a better movie in other respects.
This film will probably take a Batman Begins/Casino Royale/Trek '09 approach and re-introduce the character in a way that says: you think you know this character's origin and what he is all about, but really you don't, here is the story as it has never been told before, etc., etc. Standard issue for reviving a franchise in Hollywood these days, but that is because it works. Assuming that audiences know and understand the property already is tantamount to giving people a reason not to bother paying money to see the film.
As for Luthor, he might appear briefly towards the end of the first film, but I would look for him to be the main antagonist in the second film, like the Joker in TDK. Zod/Brainiac in the first film as part of the Kryptonian emphasis, Luthor in the second film which has Superman firmly established on earth, and then, Doomsday in the third film, which would feature the death of Superman and could really be an epic way to end the trilogy.
There are basically three stories to tell about any superhero: origin/taking up the mantle, struggle against the main antagonist, death/giving up the mantle.
Does anyone in Hollywood know how to do a proper Superman story? Why the hell can't the producers hire any good comic book writers to write the friggin story?? 
