It'd be nice to be able to manage plugins in network mode in a similar fashion to themes. I'd like to be able to upload a plugin, and by default, nobody can see it. I'd then go into something like SuperAdmin > Plugins. On this screen I could make it available (not activate) to all sites. If I don't want everyone to have that plugin as an option, I could go the SuperAdmin > Sites > Edit (selected site), and make it available to just that site.
Again, I'd envision this working very similar to how theme deployment works. Being able to control who can see plugins on a site by site basis.