In the current state of the weidu backup system, there is one really annoying thing: when the weidu create "backup" folder and create binary files which are needed for the uninstallation, weidu itself directly affecting the mod directory. I really don't like this design. In order to use the same extracted mod, players have to make sure that they will remove "backup" folder when they will copy for eg cdtweaks + setup-cdtweaks.exe from BG1EE to BG2EE. If the unaware player will forgot about this, it will cause problems for them because "backup" folder will have leftover from the previous installation. Not to mention countless re-uploading mod because author forgot to remove "backup" folder.
New proposed solution is simple: instead of "GameDir\ModName\Backup" use "GameDir\weidu-backup\ModName\"
I don't think leftovers will cause any problems. Weidu logs changes, and restores only what was changed. So it's really cosmetic.
Anyway, with BWS/Zeitgeist, soon most people won't do any moving at all. And those who will, will also probably proficient enough to handle it properly.
subtledoctor posted yet another thing which favors weidu-handled backup location. I add another: authors can seriously screw it:
BACKUP ~\KaraTur\Kbackup~
this code will create "KaraTur\Kbackup" inside root level of the drive which has IE game installed.
Even if it happened (and it didn't in 15 years, did it?), it's not the end of the world.
I agree that weidu directory layout is archaic and somewhat inconvenient, though - to the point of irritation, sometimes. With many mods, game directory is severely polluted. It's just hard to find the required files. And override is polluted with loads of marker files, too.
But if we're talking about changing it, I wouldn't stop on half-measures. Allocating one single directory for everything mod-related, and underneath it, separate dirs for mods, backups, logs, markers - that would be an improvement.
Anyway, all this is pretty low priority. People don't really have problems with current system.