User blog comment:Ygrain/EDI and the geth: their purpose in the story?/@comment-70.143.64.65-20120724065141/@comment-24174486-20120724213943

"while you can reject it implicitly you can't reject it explicitly."

Considering the circumstances, it's understandable that Shepard wouldn't try to argue with the Catalyst. A massive battle is going as on they speak, thousands of lives are being lost, Shepard themselves is critically injured, the Crucible itself is in danger of being destroy, and for all Shepard knows trying to tell the Catalyst it is wrong might anger it.

On the argument of how it is presented, let's hypothetically say that when you encounter the Catalyst, it tells you that the Reapers were created because it wanted to kill a lot of organics rather than potential organic/synthetic conflict, and everything else stays the same. Would that make the validity of killing an entire galaxy for fun the main theme of the series? (Admittedly, it is an absurd example, but it demonstrates the point that the reasoning behind the Catalyst creating the Reapers doesn't automatically become the main theme of the series.)

The Catalyst's beliefs do connect to a major theme of the series: organic/synthetic relations. But that doesn't mean that what the Catalyst believes is meant to be what the player should believe.