No need to mark spoilers in this thread, folks - it's a post-game thread so all the plot should have been revealed to anyone reading it already!

I'm pretty sure TSoL is right in saying that fal'Cie can't damage Cocoon directly, while a pretty major point of what you get out of the major dialogue with Barty/Orphan is that humans have the power to do what they wish, which is something that fal'Cie (or at least Barty) crave. The power of fal'Cie is that they are, to some extent, immortal and insanely powerful (strength-wise). The power of humans is that they are capable of making whatever choice they wish regarding what they do with their life - the fal'Cie are tied to a specific role or purpose. With this in mind, the fal'Cie create l'Cie to do the things they are unable to do. Of course, humans being able to make choices means that the fal'Cie couldn't control them directly... they had to blackmail them into doing what they want by effectively saying "if you don't do it, I'll make you into a wandering monster."