Is that right? That didn't seem to be your stance earlier. I thought the audience was supposed to "apply their own judgement, reach their own conclusions, and be able to justify their choice."
We were told from the beginning that that was the idea of the Mass Effect trilogy.
Even in fiction where the intent is to provoke discussion, if you get a particularly biased writer on the team, their opinions are going to be reflected in the writing. Hence in ME3, we don't see any sensible ME2-Mordinesque arguments for the genophage balanced against its detractors, but rather a shrill racist as its only advocate. We don't hear any mention of the extermination of the Quarian race and centuries of murderous isolationism that followed, even from the Quarians themselves; rather, we're subject to a half-hour slideshow of self-sacrificing geth throughout history, the veracity of which nobody challenges.
When the writing team takes grey issues designed to provoke discussion and shifts from neutrality to advocacy, ignoring or outright contradicting elements of established lore and disregarding past arguments to weaken one side in favor of the other (otherwise known as a strawman), people aren't all just going to bob their heads and go along with it. Hence why these issues continue to be hotly debated, even after certain writers have made their own sympathies known. Hence why some still lament that we can't continue working with Cerberus.