http://www.ligonier.org/blog/5-questions-ask-when-reading-bible/
Dear Logos. I have been begging for this since Libronix 3. Please quit being an idgit and meet the need in some reasonable manner so that the average Christian would find Logos useful and it could be used as a common platform for Bible study. I am showing this in the simplest personal implementation from which other methods could grow. What the market lacks in library size is made up for in volume.

Column 1: Reading plan - already implemented
Column 2: Bible - already implemented with many neat features
Column 3: New document type with:
- date
- passage
- study method template - simply a text box for the Journal method; the 5 questions of the Ligonier method each with their own text box plus a notes/comment box for the Ligonier 5 questions Method.
- the latter two may be repeated under the same date
Column 4: Power Lookup and Information - already implemented
There are many Bible study methods that could be done using this simple a method. You could either provide the template or allow the user to provide it.
There is another group of Bible study methods that would also need a Highlighting Palette - a feature you already have as well.
Yes, years ago you prototyped a much more complex system. While this is very much a first step, the biggest hurdle is making the text in the textbox searchable and printable. But it also has the advantage of filling the frequent request for journal capability.