Chrono Crusade/WMG

Aion is the true writer behind the anime, and it's his Fix Fic for the manga version.
Think about it: in the end, everybody dies except him. It's his revenge against those that brought about his death: Rosette and Chrono die soon after the "final" battle, Joshua (who, in the manga, aids in removing his horn and helps Chrono and Rosette in his defeat) is scarred so badly by his experiences that he's mentally a child, and Remington falls into despair and is later a witness to Aion killing the pope! This also explains other changes: Chrono is his twin brother? No--his brother would never betray him! He was just a simple demon! Chrono, when pushed too far is frighteningly powerful? Maybe, but he's lost too much of his backbone to tap into his rage! Rosette was a Badass Normal? No, she's the easily-manipulated reincarnation of Mary Magdalene! (Who was also killed off much more quickly in the anime.) Not to mention Aion got to go on more sexual escapades in the anime and just be more badass in general. Of course, he at first makes it look like the "good guys" are going to win--he's fond of dramatic tension. But in the end, he's the one that comes out on top, and makes his foes look like fools.

Aion is the CEO Gonzo and Chrono socked him in the mouth long enough for Seto no Hanayome to be as awesome as it was.

The demons are responsible for the extinction of the dinosaurs!
In the 8th volume of the manga, Azmaria gets a vision of how the demons came to earth. In the vision the demons lose control of their ship and crash land. Think about it! The ship was about the size of Manhattan Island; if something of that size had crashed into earth, it would have the effect that is accepted by most people as the end of the dinosaurs; something gigantic crashed into earth, it raised a huge amount of dust, which blocked out the sun, Etc.

Chrono Crusade (manga) is in the same universe as Bioshock
Think about it. ADAM and EVE are the remains of Legion and infusions of Legion with Astral energy that was spread over the Atlantic and Eastern Seaboard when Pandemonium was breaking up. Splicers mutated because they didn't have horns and weren't able to get enough astral energy to keep their mutations under control. Geography is feasible and there are the anachronisms. I can't quite account for the lack of the ring around the planet. Maybe the wrong time of year? Also, Dr. Tenebaum is secretly Shader.

Azmaria is really Azathoth of the Cthulhu Mythos
They both begin with "AZ", and their names make no sense! Maybe that was Aion's plan, to merge Azmaria and Azathoth, two opposites creating a explosion of awesome to restart the universe!

The island that Pandaemonium crashed into was Atlantis.
With Myth of Atlantis probably came about because of it, anyway. The island breaking apart accounts for Atlantis' mysterious disappearance, and Pandaemonium sinking to the bottom of the sea and the demons continuing to live there could explain why some versions of the myth believe that Atlantis is merely hidden under the sea.