I think Synder, Golan & Nolan will use the same template as the Batman trilogy in terms of storyline.
1st film: Origin, foe is 'one of his own', greater good theme, Ra's Al Ghul/Zod
2nd film: Hero is more established, living with consequences if his presence in Gotham/Metropolis, use of most popular villain Joker/Luther, but will be secondary villain alongside maybe Brainaic which would make sense. Lois Lane will play bigger part, maybe some sort of love triangle with Luthor, who knows.
3rd film: Both focuses on their 'death' Bane/Doomsday