So, we all know that civilization on Pulse is wiped out. Ruins and Cie'th are all that are left of the once thriving population. Why? Indications are that people had been living, and advancing, on Pulse for long before the collapse. Yet, after the War of Transgression, humanity is wiped from the surface of Pulse in a miniscule amount of time. After all, those ruins had appeared abandoned for at least a hundred years, and the War of Transgression was only about three hundred years ago. So what happened during the War that caused the end of Pulse civilization?
It wasn't the War itself, for that seemed to have little impact on Pulse. Pulse was on the verge of winning, and only failed when Ragnarok was robbed of its power. Everything we hear indicates that Cocoon never launches a counterattack, they merely repair and await another invasion.
The only thing I can think of is the Fal'cie. Specifically, Anima. Each Fal'cie was tasked with certain projects. Titan with ensuring the growth of the strongest creatures, Atomos with his digging. What if Anima was the Fal'cie charged with protecting mankind and helping them advance? When Anima was pulled from Pulse, his influence over the world went with him. No longer able to help the people, the balance of the Fal'cie's tasks were shifted, and people become crushed in the grinder, overtaxed as l'Cie, and unworthy by the standards of Fal'cie like Titan.