Wow, there's so much slick art for such a short game! I feel like you really loaded it up with a lot of customized art that most VNs would re-use for hours worth of content. It really does feel like a slice of a much larger game and honestly I would be down with that: the world is intruiging, the characters are good, the popup glossary gets you up to speed, you get to do cool stuff. And there's puzzles. And music!
Two things stood out (and I only bring these up since the rest is so good): I'd add some content about what the 'spirits' did that was so harmful; you're told that but the player should have some reason to believe (and later, understand why other people still believe) the spirits are bad news. The other thing was that the Archbishop's heel turn comes off as a little easy, he becomes a sneering villain really quickly. He's a good bad guy, but he should be trying to convince you that even if what you've learned is true, progress is still worth it. Or something similar... something that makes me think he's still a person underneath and not a cardboard cutout.
Please tell me you're making an expanded version!