Make sure you wait until after the credits.

[hollowleviathan]

For the first ten minutes I thought that I was in a computer simulation by the Toronto scientists, and that this was one of millions of automated tests, to see, just in case, whether stressful situations might help Simon's brain condition.

And this isn't something that the game told me, it wasn't a "you didn't save this character!" screen or dialogue, it was a personal realization, and another immediate realization that I had left a man screaming on the floor in pain

I think that start, where I was certain Simon wasn't real but a construct, led me to rapidly consider everyone else behaving with sentience on their own terms; they wanted to be real, well, so do I. Similarly, I noticed quickly that the WAU was preserving people, keeping them alive when you meet Amy soon after. I only unplugged one of the two, and she seemed to still be holding on...

It was thinking of them that, even after seeing all of the monstrosities possible, knowing that Simon-2, Simon-3, and Catherine were all possible, I thought the WAU was worth giving a chance and letting live when you get to the end. I agree with your assessment of the ending, as well. Utterly devastating; as it fades to black for the credits, we don't even know if the bullet launched the ARK successfully, just that you uploaded and it fired. I imagine that Simon-3, in a desperate bid to repair Catherine's Omnitool, goes back and puts it into a WAU flower.