My idea would be to have flashbacks ala the first season of lost. Even then they would be flashbacks that are pertanent to the main story. In the version i've been working on off and on the flashbacks would be more about Johnathan Kent and the lessons he taught him along with Jor -El's lesson's in the FOS . This is because the first film is about Clark's idealism meeting with reality and about Clark making mistakes and learning that he can't change the world on his own. Therefore the flashbacks that make the most sense are those that pertain to past lessons he learned and what shaped his ideas. Part two with Brainac as the villan , would feature flashbacks that focus more on Krypton's destruction and Brainac role in it , along with Jor El sending Kal El to earth. Maybe some Zod stuff hinted at for part three. Anyway those examples of how I would do the origin. That way the origin doesn't sort of delay the main story or shorten it , but serves to move the story forward. Since the movie going public knows Superman's origin , you can at least connect bits of his backstory into the main narrative instead of the main narrative being delayed for the backstory.