I know others may have wish lists also and maybe they'll add them in this thread.
I wish I could do some things in Logos..... like:
1. Have "Links to other sermons" in Sermons. I would love to be able to have links where I can quickly switch to a book or another Sermon to review something about the point I'm making in the current Sermon.
2. I would like more "Icon" choices for Notes. I would like an Icon for each letter of the Alphabet and one for Greek alphabet.
3. I would like when I create a Personal Book in Logos and I get warnings... I would like to know the line number whereby the warning occurred. This would help greatly for when I compile a personal book and get gazillion warnings... 
4. I would like to see in "Layouts" colored breaks... where I have my bible on top of page and another book on bottom of page, the bar that separates them could be a different, more recognizable color, especially in dark mode.
5. I would like an easy way of "linking Notes". For instance, I have Note 1 and want to link it to Note 2 and have Note 2 be able to link back to Note 1 and then also link to Note 3. I find I want to sometimes use my Notes to go down them in a particular order (links).
6. I would like to have "<>" in the "Table of Contents" side bar of every book whereby I can click "<" to close all book chapters or such and click ">" to expand all books and chapters and such.