The plugin directory depends on the underlying OS. Avogadro can search multiple locations, so it would be possible, for example to have {prefix}/share/OpenChemistry/Avogadro/plugin as a “shared path.”
As I said, we spent the 2.0 release concentrating on individual users - shouldn’t be hard to come up with options for a shared path. As I said, the main thing is that users will still need to see a “New Plugins Available” dialog with a list of the shared plugins to register in their personal settings file.
You should definitely try the new draw tool. If you change bond orders or change the element of an atom, the bond lengths will definitely adjust.
But I’m very curious to understand why the MM “does not reliably produce the expected geometry?” That sounds like a separate thread.