You know what would be awesome? If the evil ending from Bioshock 1 was canonical, and the good ending from Bioshock 2 was canonical. Eleanor realizes that Jack from the first game has been causing chaos up on the surface with his very own Splicer army and a bunch of submarines equipped with nuclear weapons.
He's built himself his very own Rapture city, that stretches from the bottom of the ocean up to the surface and beyond, and Eleanor must defeat him by herself to save the planet from his madness.
Since the first and second game explored both Anarchy and Communism, how about we have Jack be a fascist? He rules his empire with an iron fist, and his splicers are more dedicated than ever. He's built himself loads of Big Daddies that work independently without Little Sisters, as instead they hold both functions of collecting and storing ADAM, as well as protecting it.
Plasmids are more powerful, enemies are more diverse, and the story is, to me at least, very interesting