With the directories I was thinking it would be good to try having them in a structure similar to how they are in the database. You could then instead of having a "batchupload" have a "site update" with an option to just go through the catagories or specific albums (Large sites with thousands of pictures would take forever otherwise.)
Please have a look at PIWIGO gallery. This gallery offer to "SYNCHRONIZE" the database with directories...
http://piwigo.org/
I don't know anything about coding, but i suppose the synchronisation scan the folders, and then record in db "folder/subfolder/mypicture1.jpg" (instead of "picture1.jpg)
This is nice
=> to check pictures still in directories that we thought having deleted...
=> To add easily new albums (asking how we would manage all persmissions as i'm writting it...)
=> To keep an organisation when we would move galleries, download it from ftp, etc...
Hope this project will be possible :)