I've just realized what's wrong with Pilgrims to Ruin. In the intention to hammer on the theme, hard, I let it take choice out of the picture, forcing you to accept its theme. Effectively ruining the very potential to create theme. It doesn't let you tell a story, it forces you to tell its story. I'm like "oh shit".
Luckily, it's a really really really easy fix. A matter of changing a few sentences in the resolution rules. I think this insight has gotten me to the point where I can actually finish the game for real.