I guess what I'm feeling is that no one ever builds a house that has not first been designed and measured in every detail by an architect, first, and it seems to me that that's what I've been trying to do with Archon. I realize that writers don't always know all the details; some of them you learn while writing the story. But you do have to start, I would think, by understanding motivations and understanding why and how certain things need to happen.
In Archon, for example, I realized that one problem I had with it was that I don't believe in the Gnostic cosmology that my characters accept as absolute fact. To me, it doesn't matter if the Demiurge is not the true God--just as my character Paul finds the idea that the Demiurge is not the true God to be silly and irrelevant--and he's a priest of the Demiurge, one of the people who is instrumental in fighting heresy.
It really is not done to have one's protagonist be a hypocrite.
I realized that the story could not continue that way. The Demiurge is supposed to be the villain--or at least one of them. What the villain does and is must matter deeply to the other characters, or you don't have much of a story, at all.
So I'm working on getting much more deeply into my characters' heads and even into the Demiurge's head, so it can be more of a threat than it is, right now. I'm working out the religion more deeply, too.
Writing isn't the same as architecture, but you still need somewhat of a blueprint and a plan before you start hammering wood together.