Allow "hybrid" sorting modes
Two possibilities: the simpler one would be to permit manual sorting of the top-level folders, then alphabetic or default sorting of subfolders. The more complicated one would add a property to each folder, allowing manual sorting on a per-folder basis.
The particular scenario I just ran into was, while using manual sorting mode, creating new sub-subfolders. They sort by order of creation, rather than alphabetically. The workaround is to temporarily switch to default ordering, then create the folders, and then switch back...but this is clumsy :)
How about at least adding a "sort" context menu item to the parent folder in the "manually sort folder" dialog?
If I understand you correctly, you're suggesting that, when doing manual sort in the dialog, one can right-click on a parent folder and perform an alphabetical sort on its children. Why not? I'm not going to implement this because of a lack of time: this addon has been working just fine for the past two years, and I've never had to release an emergency version or anything, so I'd like to keep it like that.
However, feel free to submit a patch! I'd happily review it.
The code is horrible, though: I wrote that three years ago as a gigantic hack and never touched it since :)