I've been looking at text visualization in detail, and noticed that it has been some time since Faithlife took advantage of the quickly changing field of computational linguistics. This is fair warning -- I'm going to propose something concrete for semantic relations ... but I'm also thinking of theme progression. You should be too. Visualizing texts: a tool for generating thematic-progression diagrams. Do you have some favorites that aren't available?
I already recommended argument visualizations. I have that in my Bible software, and it's not particularly complicated. And scales nicely by denomination/subject, etc as well.
I just got the 3 Zondervan Advances/Rhetoric books ... many (many) more great ideas ...I didn't know questions make up such a large share of the NT.
Themes, no offense, I'm a bit leary of (though quite heavily presented in Christian resourses). Also, I'm just guessing, Logos would need something down to earth. Even discourse was and still is missing good visualization (likely limited to Logos text abilities).