It's fair to say that for power users, prioritisation is broken (though I accept it's great for most users). Given that L6 has fixed many of my previous bugbears, I felt it is time to focus on this, which has seen precisely zero improvements since L4 was released in November 2009.
All these proposals involve changes to the user interface, not the underlying architecture.
Proposal #1: Move prioritisation into a separate tool, similar to Collections. This will give users more room.
Proposal #2: Add a CTRL+F function to find existing resources in the prioritisation list. When I add a new commentary to my list, I think something like "That should do a bit lower than the BST", and then have to scroll through 360 entries trying to find the BST. I should be able to jump straight to it.
Proposal #3: Add a datatype filter to the Prioritisation Tool so that we can display only those resources that match a particular datatype (English Headword, Bible, Apostolic Fathers, etc.). If I'm prioritising the Fathers, I don't need to see the other 350 entries to do so. If all entries in the list are numbered in order, the number is retained when filtering, it will be easy to cope with situations such as adding a new resource in between resource #112 and resource #156. Just place it at #134.
These three proposals would benefit everyone. I have two additional proposals for power users.
Proposal #4: Add an optional advanced mode. The above proposals will help a lot, but power users would appreciate being able to prioritise each datatype entirely independently. The filter would be a big help, but several books have multiple datatypes, so you can move a commentary series and find it's affected your Church Fathers prioritisation. The advanced mode I'm proposing would work in a very similar way to L3's prioritisation. You would have a dropdown at the top, and choose your datatype. Then prioritise your resources underneath, just for that datatype. There would be no single list of all datatypes at all. You could switch from standard prioritisation to advanced prioritisation at any time, but not go back.
Proposal #5: Show unprioritised books. It's helpful to know which books you haven't prioritised so you can make sure you're not missing good books because you've forgotten to prioritise them. Adding the ability for users to create a collection of unprioritised books (or have one built into Logos) would make that simple.
In case you don't believe me when I say that prioritisation is broken for power users, here's a section of posts. Some of the posts contain unworkable proposals. They still prove that it's broken, even if they also prove that a fix isn't easy.