The GUI could use some refinement, particularly the Package Manager. Moving the file-related functions (View Readme etc) to the right-click menu for example.
When I pack a mod for release I use Winrar to compress the entire Data folder,
filtering for my file prefix. I then open the archive, delete any backup files that got caught in the process, and use the "Add FOMod" function in FOMM, filling in information as required.
Since the nexus doesn't allow *.fomod files I then use winrar to extract the fomod to a new folder (I have *.fomod defined as an archive in winrar, so I just right-click->extract), and re-compress with the highest compression settings. I will generally choose the zip format for compatibility.
This means I only use the most basic functionality of FOMM. I took a look at the "Create FOMod" function, and was not impressed to be honest. It makes the whole process fiddly, adding files is not intuitive at all. If it had a prefix search, that automatically arranged files in the folders I've created (as winrar does) I might consider using it.
As it is there's no reason for me to use the "Create FOMod" function