User blog comment:Ygrain/EDI and the geth: their purpose in the story?/@comment-70.143.64.65-20120724065141/@comment-99.242.69.124-20120724123119

"the final choices are all framed in terms of synthetic-organic conflict"

Each of the choices is presented by a character who believes in inevitable conflict between synthetics and organics, a character who was created to focus on that idea. Although the Catalyst is helping Shepard use the Crucible regardless of which choice Shepard wants to pick, it is a biased character and thus gives its own opinions on each choice.