I think people are making too much of the Twelve's failure and that this means Bahamut is stronger than the gods. In the end, it wasn't the Twelve, it was a mortal (I guess depending on your view of Archobs, this is debatable) who attempted to use the power of the Twelve, not the gods themselves doing it. Even Louisoix knew there was a chance it might fail, and that's why he had the last resort of making everyone disappear.