As the better popularity of WP and the growth of this community, you can expect that more plugins would be developed. Therefore I think it would be great if we have some extra features for the plugins.
Firstly, an option page for setting up config variables used in the plugins, i.e, the "xx days" option for a "close comments after xx days'' plugin. To achieve this, an extra option group would be needed as well as the mechanism (APIs) for a plugin to manipulate datas in database.
Secondly, plugins might have to store datas in the database by either using their own table or adding column to the existing one. It would also be great if some APIs are provided so that plugin developers can write some scripts to establish/delete database entries during the activation/deactivation.
The scenario, with these two features, for using a plugin would be:
1. put files in plugins directory,
2. activate the plugin in the admin panel,
3. setup/config options for the plugin in the option page,
and you have an plugin in action. Reversely, all database entries used by a plugin would be deleted when you deactivate it.
Ps. Some plugins might also have their own including files, I think there should be a directory for them as well.