mw.notifications are currently really small and honestly hard to notice on Desktop. Additionally, we have a second notification system for postEdit (and it differs in visual style for a researched / ab-tested reason).
Both systems could use a bit of a visual make-over to bring them into 2015-16.
Additionally, the two systems should probably be combined/share an api, to make it easier to target them on mobile and other different skins. Another possible usecase is for user-user messaging and other 'in page' website notifications that we currently do not yet provide but have been discussed.
The notifications could be improved to have icons like checkmarks or X's, templates, positionable and to have different 'attention' levels towards users.