Just beat the game last night, and asside from all my other gripes with the ending one thing really stood out to me.

As I understand these are the facts that we know from the game (or have to assume are true):

- Fal'Cie were created by the 'Maker'
Source: Dysley
- Fal'Cie can only do what what they are created to do
Source: Dysley and Orphan
- Fal'Cie can have desires outside of what they are created to do
Source: Orphan wanting to die even though he can't kill himself, Fal'Cie wanting the Maker back even though the Maker didn't make them to bring 'him' back
- Fal'Cie can't change when they are made to do
Source: Orphan
- Coccoon did not exist when the Maker left
Source: Dysley
- Fal'Cie build cocoon
Source: Dysley, common knowledge

Since Fal'Cie can't change their purpose and there were obviously no Cocoon building and running Fal'Cie around back then (since the idea of Cocoon didn't even exist) the only way it could have possibly been created was by making new Fal'Cie with purposes involving the construction and running of Cocoon.
To summarize: Logically Fal'Cie must be able to create other Fal'Cie with purposes different than their own.

Now:
WHY THE HELL DIDN'T THEY JUST MAKE A FAL'CIE TO KILL ORPHAN?!?!
That just strikes me as a million times more logical.