User blog comment:Ygrain/EDI and the geth: their purpose in the story?/@comment-4237253-20120723204253/@comment-24174486-20120724123939

"Also, the lack of other options than those proposed by the Catalyst strengthens this narrative error - it's at the end, there is no way out of it, it must be important."

That is not because you're meant to agree with the Catalyst or that it's a main theme of the series, but because the final choice is how to resolve the main conflict of the entire series: stopping the Reapers. There'd be no reason for Shepard to decide not to use the Crucible and stop the Reapers after everything up to that point.

The Catalyst was created to find a solution to an inevitable conflict between organics and synthetics. While it is placing helping Shepard stop the Reapers above finding a good solution to its "problem", it still places a priority on it because it was programmed to do so. It presents your choices and merely its own opinion on each of them.