Hi,
just my two cents on it.
Can't we keep the shared stuff in the home directory? It would be user-wide instead of system-wide, but already a reduction and we wouldn't need to mess with access restrictions in /usr. Possible naming: $HOME/.wine-addons-gecko $HOME/.wine-addons-mono
Another idea would be to outsource this topic to steam or even better winetricks. Most filesystems in use support hardlinks, a winetricks verb with wine prefixes as arguments that hardlinks all gecko/mono stuff in them (if their shaXXX hash match) looks very easy and suitable to me and steam could use it too. That way the prefix remains transferable.