EDIT: I just tought of an other option, maybe possible for a sequel.
5 year after Eleanor and Delta went to the surface,
- Eleanor discovered a way to revive Delta (in his suit of course)
- they send a robot down to rapture to see what it's up to.
- They discover that many of the splicers are cured by a private scientist who hid in a room while rapture was on it's edge of destruction (Bioschock 2). Yet some of the splicers still lurk around.
- When they discover that, they go back down and try to rebuild rapture.
-Big Daddies, Big Sisters and Little Sister are still there, they just can't be missed in the game. No steam-punk cyborgs? No Bioschock.