User blog comment:Matthew Paul/BioWare never made a case?/@comment-3046679-20130110160425/@comment-24174486-20130111030905

The whole "synthetics killing organics so organics won't be killed by synthetics" thing just happens to leave out how the Reapers aren't quite synthetics, or how Reaper conversion is intended to preserve organics in an ascended form. While we may not agree with the Catalyst's logic, we can't deny that an AI created by an ancient race will definitely have different views and ideas.

The ending has three different characters advocating three different options for three different reasons—those reasons being major plot arcs/themes in the series. Anderson represents the war against the Reapers, and thus represents the option of utterly destroying them. The Illusive Man is focused on humanity's place in the galaxy, and sought to control the Reapers to elevate humanity. The Catalyst, in regards to organic/synthetic relations, advocates Synthesis.

To say that the Catalyst's problem takes precedence is silly, given only one option really provides a solution to the Catalyst's problem whereas all options end the Reaper cycles. The Catalyst views each option in terms of how it affects its problem because that is what it exists to do. It is in its character—just the same as how the Illusive Man was motivated by his desire to help humanity.