If the series were to continue for a 3rd season the Light's alliance with Darksied would be explored further and what deal they have with the evil New God. After all there have been hints of New Gods as far back as season 1. He supplied the Light with Boomtubes, so he is interested in Earth like in other continuities.
***SPOILER***
The episode this morning it the Light or some of its members have taken War World and left Earth for some new plot. Savage is setting himself up to be a universal power. I imagine he won't be back for a few years in the shows time
If it where to guess what the writers would do I would say they would introduce more heroes, like Cyborg, Raven, Starfire, Kyle Rayner (Green Lantern 2814.4), Supergirl, that female Speedy to replace Artemis,make Batgirl into Oracle, replace her Cassandra Cain or Stephaine Brown, Robin III, becomes Red Robin, and replaced by Damien Wayne as Robin.
Arsenal and Static's groupmight become the Outsiders group.