Today at the Television Critics Association’s press tour to promote Alcatraz, the series executive producer talks about the series that will debut on January 16th on Fox. He revealed little about the show except to say "this show was designed as episodic with an overarching large mythology we get to over time."
He also briefly commented on the changing of show runners halfway through filming, essentially dismissing it, "[Elizabeth Sarnoff] helped the pilot get to a place that was extraordinary. "She didn’t feel like she was the right person to run the show" after creative changes were made.
The impression I get is Fox demanded the show have a villain (escaped convict) of the week format with the serialized (aka mythology part) de-emphasized. The mythology will be the reveal of how and why the inmates of Alcatraz were allowed to jump forward in time (and hopefully explain how they adjust to a new era at a fast rate). My thinking is the show's format will not be much different than The Mentalist with its mystery of the week and the occasional "mythology" of the Red John serial killer. Or if need another example of a more sci-fi bent, go with the show that created the episodic with serialized mythology format - The X-Files. JJ Abrams sales pitch for the show to TV viewers can be found here.