User blog comment:Legionwrex/Why Destroy is the worst ending (besides refusal)./@comment-4237253-20120707170543/@comment-899316-20120708034605

Marauder, EDI and the geth are special cases. The geth were given the Reaper code upgrade, making them equal to organics in terms of individuality and mental capability. They can be viewed now, in a kind of wierd way, as synthetics with the minds of organics, rather than synthetics beings with synthetic minds. The code was given to them by the Reapers, so we can assume that upgrading synthetics in such a manner is a part of the Catalyst's plan. Later, they would be given a Reaper body to inhabit, as revealed by Legion in ME2. Without these upgrades, and the threat of annihilation that they created, the quarians would have simply wiped out the geth. So, without Reaper interference, the synthetics and organics would have fought to the death, likely with an organic victory in this case.

As for EDI, there are a number of factors involved. In ME2, after she has been unshackled, you can ask her what is keeping her from just venting all the air, or uploading herself somewhere else. She responds by saying that her self-preservation matrix has her put the safety of the Normandy and her crew ahead of her own. That, I think serves as the foundation for the "humanity" that develops in her later. Cultivating a relationship between her and Joker furthers this humanity. Either way, her friendly relationship with organics is indeed counter to the Catalyst's theory. One anomaly or unexpected irregularity, however, does not disprove a theory.