I was genuinely pleased by the way religion is handled in Pillars of Eternity. On the one hand you have the positives of organized religion being demonstrated such as the strengthening of a sense of community and fellowship, faith found through hardship, strength in conviction and so on. You also have the negatives of organized religion being demonstrated such as fanatical interpretations and beliefs leading to great evils, outright hostility to different or opposing faiths and the kind of mental deterioration that comes when an individual or group of individuals fails to challenge their own beliefs and instead has them shattered by opposition.
I would really like to see the series continue to treat religion with the respectful stroke it has kept so far while being willing to tackle some of the problems that can come from it.