Would like to suggest this: have labels defined at organization level.
Why? When we have a bunch of repos, they usualy use the same labels schema (titles, colors) on all of them. With the current system (per repo) maintaining the labels can become painfull. When you add a new one, you have to go and add it on every repo. If a color changes, you have to go and edit all the repos. Etc.
Being able to define organization labels would take care of this. Repos should be able to have their own labels as they have now, of course.