While it would have been nice to have a Langrisser 2 (Der Langrisser on SFC)-style story fork, it's basically impossible to accomplish in a modern MMO, especially with a persistent story arc. You would have to lock out Prae, CM, make two separate stories, etc, etc, and then somehow slam them all into the same spot at the end. At least in a single-player RPG, ending up in a different place ends with the end of the game. In an MMO, your character is still in the game world, and you have to pull them together not only within persistent endgame content but also for future expansions.

It's worth comparing to what SWTOR did with Flashpoints. In Cademimu, light-side Imperials would intervene with "Stop killing innocent Imperial citizens!" and dark-side Imps would just say "Capitulate, whelp!", but the action would be the same -- stop the guy by any means necessary. You'll have different motivations with the same outcome because you can't afford separate outcomes with in the game world.

(Re: the gods, the definition of Good King Moggle Mog XII as a "myth made manifest" makes me wonder if the Gods will be 12 incarnations of the five races' primals.)