I have a suggestion based on my usage of the iPad app. I have come to the realization that Logos appears to be syncing ALL the notes for a particular resource each time a new highlight/note is added or edited. Performance doesn't appear to change by breaking up notes into separate note files--it appears that the accumulation of all notes for a particular resource are sync'd. This is not a problem if there are very few notes for the resource. However, as note files grow, the highlighting changes are taking anywhere from 6-14 seconds to display and performance restrictions are disruptive for simple reading and highlighting.
One solution I would recommend (based on conversations with Alabama and how the desktop version works) would be to allow the user to select which note files they would like to have sync'd and displayed for a particular resource. This would resolve performance issues (since we could then split up our notes into smaller note files and only display the ones we need), and it would also provide a greater flexibility on how we use highlighting.
Anyway, those are some of my thoughts.
Dave