As Logos attracts more Accordance users, there are some features that would make the transition a lot more comfortable for us:
1) Customizable keyboard shortcuts. It's difficult to learn the features of a new app, but being able access those features in familiar ways goes a long way toward making the process less painful.
2) Renaming Tabs. Accordance users generally work heavily with biblical languages. Many are involved in research as students and academics. That typically means they have a lot of tabs open at the same time. It's difficult to keep track of your work when you have 20 open tabs all labelled "Search."
3) Personal Books. Make the import process easier. In Accordance you can import a plain text file, .docx, or PDF, and no special tagging is required (except for simple tagging if you're creating a Bible). You can edit your imported documents after the fact if desired.
I'm sure there are more, but these are what come immediately to mind as I've been learning to use Logos. That being said, Logos is a wonderfully feature-rich application that has far exceeded my expectations.